Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr5
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 65570391
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1216948 characters in sequence are not A, C, G, or T
File 192 of 203
Found at i:61205303 original size:24 final size:24
Alignment explanation
Indices: 61205270--61205315 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
61205260 TTATTGAAGT
* * *
61205270 TTTAATTTGTTTGGAATTTTTATG
1 TTTAAATTGTTAGGAATATTTATG
61205294 TTTAAATTGTTAGGAATATTTA
1 TTTAAATTGTTAGGAATATTTA
61205316 AATTTTTGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.15, T:0.57
Consensus pattern (24 bp):
TTTAAATTGTTAGGAATATTTATG
Found at i:61206656 original size:63 final size:64
Alignment explanation
Indices: 61206578--61206705 Score: 240
Period size: 63 Copynumber: 2.0 Consensus size: 64
61206568 CAAGTTATAG
61206578 TGGAATTACAGGCTAATTCCTATATAAACAGGATAAAAGCTTAATAGAGAAGGA-TTTTTTTTT
1 TGGAATTACAGGCTAATTCCTATATAAACAGGATAAAAGCTTAATAGAGAAGGACTTTTTTTTT
*
61206641 TGGAATTACAGGCTAATTCCTATATAAACAGGATAAAAGCTTAATAGAGAATGACTTTTTTTTT
1 TGGAATTACAGGCTAATTCCTATATAAACAGGATAAAAGCTTAATAGAGAAGGACTTTTTTTTT
61206705 T
1 T
61206706 TACTTTTCTC
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
63 53 0.84
64 10 0.16
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (64 bp):
TGGAATTACAGGCTAATTCCTATATAAACAGGATAAAAGCTTAATAGAGAAGGACTTTTTTTTT
Found at i:61214649 original size:22 final size:21
Alignment explanation
Indices: 61214617--61214681 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 21
61214607 TTTATTTGAA
*
61214617 TATATAATTTAAAATATAGTTAT
1 TATA-AATTTAAAATATAATT-T
61214640 TATAAATTTAAATATATAATTT
1 TATAAATTTAAA-ATATAATTT
* *
61214662 TATATATTTGAAATA-AATTT
1 TATAAATTTAAAATATAATTT
61214682 AAGTAGAAGT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
20 5 0.13
21 3 0.08
22 19 0.50
23 11 0.29
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (21 bp):
TATAAATTTAAAATATAATTT
Found at i:61216066 original size:17 final size:17
Alignment explanation
Indices: 61216044--61216107 Score: 67
Period size: 17 Copynumber: 3.6 Consensus size: 17
61216034 AATCTTAGAG
61216044 TTCTAATTGTATACAAC
1 TTCTAATTGTATACAAC
* *
61216061 TTCTAATTGTGT-CTTAGAG
1 TTCTAATTGTATAC--A-AC
61216080 TTCTAATTGTATACAAC
1 TTCTAATTGTATACAAC
*
61216097 TTTTAATTGTA
1 TTCTAATTGTA
61216108 GCCTTTGATG
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
16 1 0.03
17 22 0.58
18 2 0.05
19 12 0.32
20 1 0.03
ACGTcount: A:0.30, C:0.12, G:0.11, T:0.47
Consensus pattern (17 bp):
TTCTAATTGTATACAAC
Found at i:61216083 original size:36 final size:36
Alignment explanation
Indices: 61216036--61216106 Score: 133
Period size: 36 Copynumber: 2.0 Consensus size: 36
61216026 GATTATGTAA
61216036 TCTTAGAGTTCTAATTGTATACAACTTCTAATTGTG
1 TCTTAGAGTTCTAATTGTATACAACTTCTAATTGTG
*
61216072 TCTTAGAGTTCTAATTGTATACAACTTTTAATTGT
1 TCTTAGAGTTCTAATTGTATACAACTTCTAATTGT
61216107 AGCCTTTGAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.28, C:0.13, G:0.13, T:0.46
Consensus pattern (36 bp):
TCTTAGAGTTCTAATTGTATACAACTTCTAATTGTG
Found at i:61216085 original size:19 final size:19
Alignment explanation
Indices: 61216035--61216091 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
61216025 TGATTATGTA
61216035 ATCTTAGAGTTCTAATTGT
1 ATCTTAGAGTTCTAATTGT
*
61216054 ATAC--A-ACTTCTAATTGT
1 AT-CTTAGAGTTCTAATTGT
*
61216071 GTCTTAGAGTTCTAATTGT
1 ATCTTAGAGTTCTAATTGT
61216090 AT
1 AT
61216092 ACAACTTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
16 1 0.03
17 12 0.40
18 2 0.07
19 14 0.47
20 1 0.03
ACGTcount: A:0.28, C:0.12, G:0.14, T:0.46
Consensus pattern (19 bp):
ATCTTAGAGTTCTAATTGT
Found at i:61216386 original size:48 final size:48
Alignment explanation
Indices: 61216309--61216405 Score: 131
Period size: 48 Copynumber: 2.0 Consensus size: 48
61216299 CTTGAGGGAA
*
61216309 TTCTATTGAATCCTTTATCATTGCAAGTTAGGCCGACTTAGGCATTTT
1 TTCTATTGAATCCTTTATCATTGCAAGTTAGGCCGACTCAGGCATTTT
* * * * * *
61216357 TTCTGTTGAATCTTTTATCCTTGCGAGTTAGGCTGACTCAGGCGTTTT
1 TTCTATTGAATCCTTTATCATTGCAAGTTAGGCCGACTCAGGCATTTT
61216405 T
1 T
61216406 AAGCAAAGAA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.19, C:0.19, G:0.20, T:0.43
Consensus pattern (48 bp):
TTCTATTGAATCCTTTATCATTGCAAGTTAGGCCGACTCAGGCATTTT
Found at i:61221202 original size:17 final size:17
Alignment explanation
Indices: 61221180--61221243 Score: 67
Period size: 17 Copynumber: 3.6 Consensus size: 17
61221170 AATCTTAGAG
61221180 TTCTAATTGTATACAGC
1 TTCTAATTGTATACAGC
* *
61221197 TTCTAATTGTGT-CTTAGAG
1 TTCTAATTGTATAC--AG-C
61221216 TTCTAATTGTATACAGC
1 TTCTAATTGTATACAGC
*
61221233 TTTTAATTGTA
1 TTCTAATTGTA
61221244 GCCTTTGATG
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
16 1 0.03
17 21 0.55
18 4 0.11
19 11 0.29
20 1 0.03
ACGTcount: A:0.27, C:0.12, G:0.14, T:0.47
Consensus pattern (17 bp):
TTCTAATTGTATACAGC
Found at i:61221219 original size:36 final size:36
Alignment explanation
Indices: 61221172--61221242 Score: 133
Period size: 36 Copynumber: 2.0 Consensus size: 36
61221162 GATTATGTAA
61221172 TCTTAGAGTTCTAATTGTATACAGCTTCTAATTGTG
1 TCTTAGAGTTCTAATTGTATACAGCTTCTAATTGTG
*
61221208 TCTTAGAGTTCTAATTGTATACAGCTTTTAATTGT
1 TCTTAGAGTTCTAATTGTATACAGCTTCTAATTGT
61221243 AGCCTTTGAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.25, C:0.13, G:0.15, T:0.46
Consensus pattern (36 bp):
TCTTAGAGTTCTAATTGTATACAGCTTCTAATTGTG
Found at i:61221221 original size:19 final size:19
Alignment explanation
Indices: 61221171--61221227 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
61221161 TGATTATGTA
61221171 ATCTTAGAGTTCTAATTGT
1 ATCTTAGAGTTCTAATTGT
*
61221190 ATAC--AG-CTTCTAATTGT
1 AT-CTTAGAGTTCTAATTGT
*
61221207 GTCTTAGAGTTCTAATTGT
1 ATCTTAGAGTTCTAATTGT
61221226 AT
1 AT
61221228 ACAGCTTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
16 1 0.03
17 11 0.37
18 4 0.13
19 13 0.43
20 1 0.03
ACGTcount: A:0.26, C:0.12, G:0.16, T:0.46
Consensus pattern (19 bp):
ATCTTAGAGTTCTAATTGT
Found at i:61221523 original size:49 final size:49
Alignment explanation
Indices: 61221448--61221542 Score: 163
Period size: 49 Copynumber: 1.9 Consensus size: 49
61221438 AAGGGAATTC
61221448 TGTTGAATCCTTTATCATTGCAAGTTAGGCCGACTTAGGCGTTTTTTTT
1 TGTTGAATCCTTTATCATTGCAAGTTAGGCCGACTTAGGCGTTTTTTTT
* * *
61221497 TGTTGAATCCTTTATCATTGCGAGTTAGGCTGGCTTAGGCGTTTTT
1 TGTTGAATCCTTTATCATTGCAAGTTAGGCCGACTTAGGCGTTTTT
61221543 AAGCAAAGAA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 43 1.00
ACGTcount: A:0.17, C:0.16, G:0.23, T:0.44
Consensus pattern (49 bp):
TGTTGAATCCTTTATCATTGCAAGTTAGGCCGACTTAGGCGTTTTTTTT
Found at i:61221720 original size:25 final size:26
Alignment explanation
Indices: 61221666--61221722 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 26
61221656 GTATGTAAAT
*
61221666 TATATAATATAAAAATACATAAGTATG
1 TATATAATATAAAAATACAT-AGTACG
*
61221693 TATAT-ATATAAAAAATCCAT-GTACG
1 TATATAATAT-AAAAATACATAGTACG
61221718 TATAT
1 TATAT
61221723 GCATATATCA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 9 0.33
26 4 0.15
27 14 0.52
ACGTcount: A:0.51, C:0.07, G:0.07, T:0.35
Consensus pattern (26 bp):
TATATAATATAAAAATACATAGTACG
Found at i:61229263 original size:26 final size:27
Alignment explanation
Indices: 61229222--61229273 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 27
61229212 CAAACAGATC
* *
61229222 CCAAATACCCACTTAACCTAGTCCAAA
1 CCAAATACCCAATTAACCTAGCCCAAA
61229249 CCAAA-ACCCAATTAACCTAGCCCAA
1 CCAAATACCCAATTAACCTAGCCCAA
61229274 CTAATGTGGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 18 0.78
27 5 0.22
ACGTcount: A:0.42, C:0.38, G:0.04, T:0.15
Consensus pattern (27 bp):
CCAAATACCCAATTAACCTAGCCCAAA
Found at i:61236483 original size:25 final size:25
Alignment explanation
Indices: 61236413--61236483 Score: 63
Period size: 25 Copynumber: 2.8 Consensus size: 25
61236403 AAGGCTTCCT
* * *
61236413 AAAT-AATACGCCACATAGACTTTTC
1 AAATAAAT-CGCCACAAAGGCTTTAC
* *
61236438 AAATAAATCGCCATAAGGGCTTTAC
1 AAATAAATCGCCACAAAGGCTTTAC
* *
61236463 AGATAACTCGCCACAAAGGCT
1 AAATAAATCGCCACAAAGGCT
61236484 CTATTTGGTT
Statistics
Matches: 36, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
25 33 0.92
26 3 0.08
ACGTcount: A:0.39, C:0.24, G:0.14, T:0.23
Consensus pattern (25 bp):
AAATAAATCGCCACAAAGGCTTTAC
Found at i:61243472 original size:5 final size:5
Alignment explanation
Indices: 61243462--61243487 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
61243452 ATATCTACCT
61243462 AACCC AACCC AACCC AACCC AACCC A
1 AACCC AACCC AACCC AACCC AACCC A
61243488 TACAAATGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.58, G:0.00, T:0.00
Consensus pattern (5 bp):
AACCC
Found at i:61243701 original size:13 final size:14
Alignment explanation
Indices: 61243671--61243705 Score: 54
Period size: 13 Copynumber: 2.5 Consensus size: 14
61243661 ATTCAAGCAA
61243671 TCAATCAATAGTAAT
1 TCAATCAATAG-AAT
61243686 TCAATCAATA-AAT
1 TCAATCAATAGAAT
61243699 TCAATCA
1 TCAATCA
61243706 TTCATATATC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 10 0.50
15 10 0.50
ACGTcount: A:0.49, C:0.17, G:0.03, T:0.31
Consensus pattern (14 bp):
TCAATCAATAGAAT
Found at i:61245047 original size:6 final size:6
Alignment explanation
Indices: 61245013--61245046 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
61245003 TTTTTTAAAT
*
61245013 AAATTC AAATTC AAATTC AAATTC AAATAC AAAT
1 AAATTC AAATTC AAATTC AAATTC AAATTC AAAT
61245047 AGAAATCTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.29
Consensus pattern (6 bp):
AAATTC
Found at i:61245052 original size:18 final size:18
Alignment explanation
Indices: 61245013--61245052 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
61245003 TTTTTTAAAT
* *
61245013 AAATTCAAATTCAAATTC
1 AAATTCAAATACAAATAC
*
61245031 AAATTCAAATACAAATAG
1 AAATTCAAATACAAATAC
61245049 AAAT
1 AAAT
61245053 CTATATCGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.57, C:0.12, G:0.03, T:0.28
Consensus pattern (18 bp):
AAATTCAAATACAAATAC
Found at i:61245141 original size:19 final size:20
Alignment explanation
Indices: 61245117--61245155 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
61245107 TCTTAATAGA
61245117 ATTTATCCTC-ATTCTTTCT
1 ATTTATCCTCTATTCTTTCT
* *
61245136 ATTTATTCTCTATTTTTTCT
1 ATTTATCCTCTATTCTTTCT
61245156 TCAAAACCCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.15, C:0.21, G:0.00, T:0.64
Consensus pattern (20 bp):
ATTTATCCTCTATTCTTTCT
Found at i:61245437 original size:22 final size:23
Alignment explanation
Indices: 61245403--61245447 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
61245393 TGTGAACAGT
* *
61245403 ATAATATGTGAAC-CTAGAGGAA
1 ATAACATGCGAACACTAGAGGAA
*
61245425 ATAACATGCGAACACTATAGGAA
1 ATAACATGCGAACACTAGAGGAA
61245448 TTGTAATGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.47, C:0.13, G:0.20, T:0.20
Consensus pattern (23 bp):
ATAACATGCGAACACTAGAGGAA
Found at i:61245479 original size:21 final size:20
Alignment explanation
Indices: 61245453--61245507 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
61245443 AGGAATTGTA
*
61245453 ATGTGAACACTTAGAAGTTAT
1 ATGTGAAC-CTTAGAAATTAT
*
61245474 ATGTGAACCCATAGAAATTAT
1 ATGTGAA-CCTTAGAAATTAT
*
61245495 ATGCGAACCTTAG
1 ATGTGAACCTTAG
61245508 CTGTTTAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 5 0.17
21 23 0.79
22 1 0.03
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (20 bp):
ATGTGAACCTTAGAAATTAT
Found at i:61250608 original size:20 final size:21
Alignment explanation
Indices: 61250571--61250609 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
61250561 AAAAATTGGG
*
61250571 AAATATTATTTTGAAAAATAA
1 AAATATTATTTAGAAAAATAA
61250592 AAATATT-TTTAGAAAAAT
1 AAATATTATTTAGAAAAAT
61250610 TAATTTTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.38
Consensus pattern (21 bp):
AAATATTATTTAGAAAAATAA
Found at i:61258498 original size:25 final size:24
Alignment explanation
Indices: 61258452--61258499 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
61258442 TGTTTTAAAT
61258452 ATATCATTTAAAATTAACATTTTA
1 ATATCATTTAAAATTAACATTTTA
61258476 ATATC-TTTAAAATTTTAACATTTT
1 ATATCATTTAAAA--TTAACATTTT
61258500 TAGATAATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 7 0.32
24 5 0.23
25 10 0.45
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (24 bp):
ATATCATTTAAAATTAACATTTTA
Found at i:61258783 original size:10 final size:10
Alignment explanation
Indices: 61258768--61258797 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
61258758 ATGCCAAAAG
61258768 AAGAACAACA
1 AAGAACAACA
61258778 AAGAACAACA
1 AAGAACAACA
61258788 AAGAACAACA
1 AAGAACAACA
61258798 GAAAGAGCGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.70, C:0.20, G:0.10, T:0.00
Consensus pattern (10 bp):
AAGAACAACA
Found at i:61262356 original size:44 final size:44
Alignment explanation
Indices: 61262296--61262384 Score: 133
Period size: 44 Copynumber: 2.0 Consensus size: 44
61262286 AGGTATAAGC
* * *
61262296 AACACCGAACTAGTTTTACAATGAGTTGAGAGAAGCATAATTGA
1 AACACCGAACTAGTTTTACAAGGAGTTAAGAGAAGCATAACTGA
* *
61262340 AACATCGAACTGGTTTTACAAGGAGTTAAGAGAAGCATAACTGA
1 AACACCGAACTAGTTTTACAAGGAGTTAAGAGAAGCATAACTGA
61262384 A
1 A
61262385 GCTATAAATT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.42, C:0.13, G:0.21, T:0.24
Consensus pattern (44 bp):
AACACCGAACTAGTTTTACAAGGAGTTAAGAGAAGCATAACTGA
Found at i:61267071 original size:24 final size:24
Alignment explanation
Indices: 61267050--61267096 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
61267040 AAACATTAGG
61267050 CAGAAATATGGTACTCACATTAAC
1 CAGAAATATGGTACTCACATTAAC
*
61267074 CAGAAATATGGTACTCGCATTAA
1 CAGAAATATGGTACTCACATTAA
61267097 TACAGACAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.26
Consensus pattern (24 bp):
CAGAAATATGGTACTCACATTAAC
Found at i:61267269 original size:44 final size:44
Alignment explanation
Indices: 61267216--61267303 Score: 158
Period size: 44 Copynumber: 2.0 Consensus size: 44
61267206 TAAGCAAAAT
61267216 ACAGCCAAACAGAAAATGAAGTTACCCAGATTAACCAAAAACAA
1 ACAGCCAAACAGAAAATGAAGTTACCCAGATTAACCAAAAACAA
* *
61267260 ACAGCCAAACAGAAAATGAAGTTACCCGGATTAACCAGAAACAA
1 ACAGCCAAACAGAAAATGAAGTTACCCAGATTAACCAAAAACAA
61267304 GCAGACAGAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.52, C:0.23, G:0.14, T:0.11
Consensus pattern (44 bp):
ACAGCCAAACAGAAAATGAAGTTACCCAGATTAACCAAAAACAA
Found at i:61267504 original size:19 final size:19
Alignment explanation
Indices: 61267480--61267529 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
61267470 GGTGGATCGG
*
61267480 TGGAGGTGGATCAGTGGAC
1 TGGAGGAGGATCAGTGGAC
*
61267499 TGGAGGAGGATCTGTGGAC
1 TGGAGGAGGATCAGTGGAC
61267518 TGGAGGAGGATC
1 TGGAGGAGGATC
61267530 GGTATTTTGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.22, C:0.10, G:0.48, T:0.20
Consensus pattern (19 bp):
TGGAGGAGGATCAGTGGAC
Found at i:61268129 original size:18 final size:19
Alignment explanation
Indices: 61268096--61268131 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
61268086 TGTAATACAA
61268096 AAAATGAAAAATAATTAAT
1 AAAATGAAAAATAATTAAT
*
61268115 AAAAT-AAAGATAATTAA
1 AAAATGAAAAATAATTAA
61268132 AATTATTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.25
Consensus pattern (19 bp):
AAAATGAAAAATAATTAAT
Found at i:61268173 original size:15 final size:16
Alignment explanation
Indices: 61268153--61268183 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
61268143 ATTACTATTA
61268153 ATAAAATAA-TATAAT
1 ATAAAATAATTATAAT
61268168 ATAAAATAATTATAAT
1 ATAAAATAATTATAAT
61268184 TATTTTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
ATAAAATAATTATAAT
Found at i:61268177 original size:49 final size:52
Alignment explanation
Indices: 61268103--61268205 Score: 142
Period size: 49 Copynumber: 2.0 Consensus size: 52
61268093 CAAAAAATGA
61268103 AAAATAATTAATAAAATAAAGATAATTAAAATTA-TTTTATATTACTATTAAT
1 AAAATAATTAATAAAATAAAGATAATTAAAATTATTTTTATATTA-TATTAAT
* * *
61268155 AAAATAA-T-ATAATATAAA-ATAATTATAATTATTTTTATTTTATATTAAT
1 AAAATAATTAATAAAATAAAGATAATTAAAATTATTTTTATATTATATTAAT
61268204 AA
1 AA
61268206 TATTTTATCA
Statistics
Matches: 47, Mismatches: 3, Indels: 5
0.85 0.05 0.09
Matches are distributed among these distances:
49 21 0.45
50 18 0.38
51 1 0.02
52 7 0.15
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (52 bp):
AAAATAATTAATAAAATAAAGATAATTAAAATTATTTTTATATTATATTAAT
Found at i:61274451 original size:90 final size:91
Alignment explanation
Indices: 61274296--61274481 Score: 302
Period size: 90 Copynumber: 2.0 Consensus size: 91
61274286 AAATTTAGGT
* * * *
61274296 TTTGGGAACCCAATGGCCGGCACTACCTAGTGTTTTGTCCCCATGATTGCCTGTTGATTGTGTCA
1 TTTGGGAACCCAATGACCGGCACTACCTAGTGTTTTGGCCCCATGATTGCCTGATGATTGAGTCA
61274361 GGCTTT-AAAAAATAATTTTTTTGAG
66 GGCTTTAAAAAAATAATTTTTTTGAG
* *
61274386 TTTGGGAACCCAATGACCGGCACTACCTAGTGTTTTGGCCTCATTATTGCCTGATGATTGAGTCA
1 TTTGGGAACCCAATGACCGGCACTACCTAGTGTTTTGGCCCCATGATTGCCTGATGATTGAGTCA
61274451 GGCTTTAAAAAAAATAATTTTTTTGAG
66 GGCTTT-AAAAAAATAATTTTTTTGAG
61274478 TTTG
1 TTTG
61274482 TGAATCCATT
Statistics
Matches: 88, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
90 65 0.74
92 23 0.26
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.37
Consensus pattern (91 bp):
TTTGGGAACCCAATGACCGGCACTACCTAGTGTTTTGGCCCCATGATTGCCTGATGATTGAGTCA
GGCTTTAAAAAAATAATTTTTTTGAG
Found at i:61275586 original size:99 final size:100
Alignment explanation
Indices: 61275443--61275712 Score: 309
Period size: 102 Copynumber: 2.7 Consensus size: 100
61275433 TTTAATTAAA
* * * *
61275443 TGTACTTGGTGCTA-GCCATTACATGGGCAGTACCAATTTTTTTTTGAAATACACTGGTGCCGAC
1 TGTACTTGGTGC-AGGCCATTACATGGCCAGCACCAAATTTTTTTTAAAATACACTGGTGCCGAC
* *
61275507 CATCAATGTT-AAAAAAA-ACATTGAGAGTCGAAAT
65 CATCAATGTTCAAAAAAATACATTGAGAGCCAAAAT
61275541 TGTACTTGGTGCAGGCCATTACATGGCCAGCACCCAAATTGTTTTTT-AAATACACTGGTGCCG-
1 TGTACTTGGTGCAGGCCATTACATGGCCAGCA-CCAAATT-TTTTTTAAAATACACTGGTGCCGA
* * *
61275604 CCTAGCAATGTTCCAAAAAAATGCATTGGGAGCCAAAAT
64 CC-ATCAATGTT-CAAAAAAATACATTGAGAGCCAAAAT
* * * * *
61275643 TGTACTTGGTGCCGACCATTACATGGCCTA-CACCTAATTTTATTTTAAAATACACTGATACCGA
1 TGTACTTGGTGCAGGCCATTACATGGCC-AGCACCAAATTTT-TTTTAAAATACACTGGTGCCGA
61275707 CCATCA
64 CCATCA
61275713 GTGTCCCAAA
Statistics
Matches: 147, Mismatches: 14, Indels: 18
0.82 0.08 0.10
Matches are distributed among these distances:
97 1 0.01
98 30 0.20
99 30 0.20
100 8 0.05
101 17 0.12
102 58 0.39
103 3 0.02
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.29
Consensus pattern (100 bp):
TGTACTTGGTGCAGGCCATTACATGGCCAGCACCAAATTTTTTTTAAAATACACTGGTGCCGACC
ATCAATGTTCAAAAAAATACATTGAGAGCCAAAAT
Found at i:61276143 original size:18 final size:17
Alignment explanation
Indices: 61276109--61276147 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
61276099 GAAATTCTTA
61276109 TTATTTATATAATTATT
1 TTATTTATATAATTATT
61276126 GTTATTTCATATAA-TATT
1 -TTATTT-ATATAATTATT
61276144 TTAT
1 TTAT
61276148 CATATTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 4 0.20
18 10 0.50
19 6 0.30
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (17 bp):
TTATTTATATAATTATT
Found at i:61277478 original size:23 final size:23
Alignment explanation
Indices: 61277444--61277494 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
61277434 ATAATGCCTT
*
61277444 TGTAATATCCCGAAAATTACTAC
1 TGTAATACCCCGAAAATTACTAC
61277467 TGTAATACCCCGAAAATTACTAC
1 TGTAATACCCCGAAAATTACTAC
*
61277490 AGTAA
1 TGTAA
61277495 GAAAGTAGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.41, C:0.22, G:0.10, T:0.27
Consensus pattern (23 bp):
TGTAATACCCCGAAAATTACTAC
Found at i:61280471 original size:20 final size:20
Alignment explanation
Indices: 61280446--61280484 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
61280436 AGCGGTGGTG
61280446 ACATAATTAAATCCACTAAT
1 ACATAATTAAATCCACTAAT
61280466 ACATAATTAAATCCACTAA
1 ACATAATTAAATCCACTAA
61280485 CTTTTGGGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.51, C:0.21, G:0.00, T:0.28
Consensus pattern (20 bp):
ACATAATTAAATCCACTAAT
Found at i:61287641 original size:26 final size:26
Alignment explanation
Indices: 61287594--61287649 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 26
61287584 ATAATTAGAT
* *
61287594 AAAAATAAATAACTAAAATAAA-CAA
1 AAAAATAAAAAAATAAAATAAATCAA
* *
61287619 GAAAAATAAAAAAATGAATTAAATCAA
1 -AAAAATAAAAAAATAAAATAAATCAA
61287646 AAAA
1 AAAA
61287650 CGAGTCAGGA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
26 22 0.88
27 3 0.12
ACGTcount: A:0.75, C:0.05, G:0.04, T:0.16
Consensus pattern (26 bp):
AAAAATAAAAAAATAAAATAAATCAA
Found at i:61288777 original size:28 final size:28
Alignment explanation
Indices: 61288733--61288791 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 28
61288723 AGGATATTTT
61288733 TTTTCAAAGTTCTCCACAAAGACTATTC
1 TTTTCAAAGTTCTCCACAAAGACTATTC
*
61288761 TTTTCAAA-TTTTGCCACAAAGACTATTC
1 TTTTCAAAGTTCT-CCACAAAGACTATTC
61288789 TTT
1 TTT
61288792 CCTATCGTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 3 0.10
28 26 0.90
ACGTcount: A:0.31, C:0.22, G:0.07, T:0.41
Consensus pattern (28 bp):
TTTTCAAAGTTCTCCACAAAGACTATTC
Found at i:61289448 original size:3 final size:3
Alignment explanation
Indices: 61289440--61289490 Score: 93
Period size: 3 Copynumber: 16.7 Consensus size: 3
61289430 GAAAAGAAAT
61289440 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG TAAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG -AAG
61289489 AA
1 AA
61289491 CCCCCTTTAA
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 44 0.94
4 3 0.06
ACGTcount: A:0.67, C:0.00, G:0.31, T:0.02
Consensus pattern (3 bp):
AAG
Found at i:61290375 original size:17 final size:18
Alignment explanation
Indices: 61290350--61290384 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
61290340 AGGATTGCAA
*
61290350 GTTTTCATTTC-ATTTTT
1 GTTTCCATTTCTATTTTT
61290367 GTTTCCATTTCTATTTTT
1 GTTTCCATTTCTATTTTT
61290385 ACAAACCTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.11, C:0.14, G:0.06, T:0.69
Consensus pattern (18 bp):
GTTTCCATTTCTATTTTT
Found at i:61297369 original size:20 final size:20
Alignment explanation
Indices: 61297344--61297386 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
61297334 GAAGAAAGAA
61297344 TTATTCATTTGAAAAGTTAG
1 TTATTCATTTGAAAAGTTAG
61297364 TTATTCATTTGAAAAGTTAG
1 TTATTCATTTGAAAAGTTAG
61297384 TTA
1 TTA
61297387 AGTTGTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.35, C:0.05, G:0.14, T:0.47
Consensus pattern (20 bp):
TTATTCATTTGAAAAGTTAG
Found at i:61299257 original size:25 final size:25
Alignment explanation
Indices: 61299194--61299265 Score: 90
Period size: 25 Copynumber: 2.9 Consensus size: 25
61299184 GAACACACCA
61299194 CAGCTCGCATGAGCTTCCCATTATT
1 CAGCTCGCATGAGCTTCCCATTATT
* * *
61299219 CAACTCACATGAGCTTCCCGTTATT
1 CAGCTCGCATGAGCTTCCCATTATT
* * *
61299244 CAGCTCGGAGGAGCTTTCCATT
1 CAGCTCGCATGAGCTTCCCATT
61299266 TATAGCTTGT
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.21, C:0.31, G:0.18, T:0.31
Consensus pattern (25 bp):
CAGCTCGCATGAGCTTCCCATTATT
Found at i:61303856 original size:24 final size:25
Alignment explanation
Indices: 61303829--61303908 Score: 65
Period size: 25 Copynumber: 3.2 Consensus size: 25
61303819 GTACTTGTAT
* *
61303829 GCTCATATGAGTTGTA-AACGAGAA
1 GCTCATATGAGCTGAATAACGAGAA
* *
61303853 GCTCATGTGAGCTGAATAACGGGAA
1 GCTCATATGAGCTGAATAACGAGAA
* ** *
61303878 GCTCGTGCGAGTTGAATAAC-AGGAA
1 GCTCATATGAGCTGAATAACGA-GAA
61303903 GCTCAT
1 GCTCAT
61303909 GCGAGCTGTG
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
24 13 0.29
25 32 0.71
ACGTcount: A:0.33, C:0.16, G:0.29, T:0.23
Consensus pattern (25 bp):
GCTCATATGAGCTGAATAACGAGAA
Found at i:61303879 original size:25 final size:25
Alignment explanation
Indices: 61303845--61303916 Score: 99
Period size: 25 Copynumber: 2.9 Consensus size: 25
61303835 ATGAGTTGTA
* *
61303845 AACGAGAAGCTCATGTGAGCTGAAT
1 AACGGGAAGCTCATGCGAGCTGAAT
* *
61303870 AACGGGAAGCTCGTGCGAGTTGAAT
1 AACGGGAAGCTCATGCGAGCTGAAT
*
61303895 AACAGGAAGCTCATGCGAGCTG
1 AACGGGAAGCTCATGCGAGCTG
61303917 TGGTGTGTCC
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.32, C:0.18, G:0.32, T:0.18
Consensus pattern (25 bp):
AACGGGAAGCTCATGCGAGCTGAAT
Found at i:61310936 original size:25 final size:24
Alignment explanation
Indices: 61310882--61310969 Score: 79
Period size: 25 Copynumber: 3.6 Consensus size: 24
61310872 GTACTTATAT
* *
61310882 GCTCATACGAGCTGTAA-ATGGGAA
1 GCTCATGCGAGCTG-AATAAGGGAA
*
61310906 GCTCATGTGAGCTGAATAACGGGAA
1 GCTCATGCGAGCTGAATAA-GGGAA
* * *
61310931 GTTCATGCAAGTTGAATAAGAGGAA
1 GCTCATGCGAGCTGAATAAG-GGAA
*
61310956 GCTCATGGGAGCTG
1 GCTCATGCGAGCTG
61310970 TGGTGTGTCC
Statistics
Matches: 50, Mismatches: 11, Indels: 5
0.76 0.17 0.08
Matches are distributed among these distances:
23 2 0.04
24 14 0.28
25 34 0.68
ACGTcount: A:0.32, C:0.15, G:0.32, T:0.22
Consensus pattern (24 bp):
GCTCATGCGAGCTGAATAAGGGAA
Found at i:61316330 original size:23 final size:23
Alignment explanation
Indices: 61316276--61316330 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 23
61316266 ATTCATATAC
*
61316276 TTAGAATTTAATCTTTTTTATTT
1 TTAGAATTTAATCTTTTATATTT
*
61316299 TTGAAAATTTAATTCTTTTATA-TT
1 TT-AGAATTTAA-TCTTTTATATTT
61316323 TTAGAATT
1 TTAGAATT
61316331 ATAGTTTTAC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 7 0.26
24 12 0.44
25 8 0.30
ACGTcount: A:0.31, C:0.04, G:0.05, T:0.60
Consensus pattern (23 bp):
TTAGAATTTAATCTTTTATATTT
Found at i:61321894 original size:88 final size:87
Alignment explanation
Indices: 61321711--61322213 Score: 467
Period size: 88 Copynumber: 5.7 Consensus size: 87
61321701 GAAATGATAT
* * * *
61321711 TCTTAAATCGCTAACACTAAAATTCTAAAAATCTTTGAAGTTTGAAAGGTTGTGATCTTAAATCG
1 TCTTAAATCGCTAACTCTAAGATTCTAAAAATCCTTGAAGTTTG-AAGGTTGCGATCTTAAATCG
* * *
61321776 GCAAACCTTAAAAGG-GAGTCACGA
65 ACGAACCTT-AAAGGAGAGTCA-TA
* * * * *
61321800 TGTTAAATCGCTAACTCTAAGATTCTGAAAATCCTTGAATTTTAAAGGTTGCGATTTTAAATCGA
1 TCTTAAATCGCTAACTCTAAGATTCTAAAAATCCTTGAAGTTTGAAGGTTGCGATCTTAAATCGA
* * *
61321865 TGAACCTTAAATGAAAGTCCATA
66 CGAACCTTAAAGGAGAGT-CATA
* * * *
61321888 TCTTAAATTGCTAACGCTAAGATTCTGAAAATCCTTAAAGTTTGAAGGTTGCGATCTTAAATC-A
1 TCTTAAATCGCTAACTCTAAGATTCTAAAAATCCTTGAAGTTTGAAGGTTGCGATCTTAAATCGA
*
61321952 GTGAACCTTAAAGGAGAGTTGCA-A
66 -CGAACCTTAAAGGAGAG-T-CATA
* * * * * *
61321976 TTTTAAATCGTTAAGTCTAAGATTCTAAAAATCCTTGAAGTTTGAAGGTTGTGATCTTAAATTGG
1 TCTTAAATCGCTAACTCTAAGATTCTAAAAATCCTTGAAGTTTGAAGGTTGCGATCTTAAATCGA
* * * *
61322041 CAAACCTTAAAGGGGACTCGTGA
66 CGAACCTTAAAGGAGAGTCAT-A
* * * * * * *
61322064 TCTTAAACCTCTAACTCTAAGATTCTAAATATTCTTGGATTTTGAAGGTTGCAATCTTAAATC-A
1 TCTTAAATCGCTAACTCTAAGATTCTAAAAATCCTTGAAGTTTGAAGGTTGCGATCTTAAATCGA
* *
61322128 GCAAACCTTAAA-GAGGAGTCGTGA
66 -CGAACCTTAAAGGA-GAGTCAT-A
* * * * * *
61322152 TCTTAAATCACTAACTCTATGATTATCAAAATCTTTGAAGTTTGAAGGTTGTGATCTTAAAT
1 TCTTAAATCGCTAACTCTAAGATTCTAAAAATCCTTGAAGTTTGAAGGTTGCGATCTTAAAT
61322214 AACAACTCAA
Statistics
Matches: 338, Mismatches: 67, Indels: 19
0.80 0.16 0.04
Matches are distributed among these distances:
86 1 0.00
87 7 0.02
88 288 0.85
89 42 0.12
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (87 bp):
TCTTAAATCGCTAACTCTAAGATTCTAAAAATCCTTGAAGTTTGAAGGTTGCGATCTTAAATCGA
CGAACCTTAAAGGAGAGTCATA
Found at i:61322195 original size:264 final size:264
Alignment explanation
Indices: 61321713--61322213 Score: 652
Period size: 264 Copynumber: 1.9 Consensus size: 264
61321703 AATGATATTC
*
61321713 TTAAATCGCTAACACTAAAATTCTAAAAATCTTTGAAGTTTGAAAGGTTGTGATCTTAAATCGGC
1 TTAAATCGCTAACACTAAAATTCTAAAAATCCTTGAAGTTTGAAAGGTTGTGATCTTAAATCGGC
* * *
61321778 AAACCTTAAAAGGGAGTCACGATGTTAAATCGCTAACTCTAAGATTCTGAAAATCCTTGAATTTT
66 AAACCTTAAAAGGGACTCACGATCTTAAACCGCTAACTCTAAGATTCTGAAAATCCTTGAATTTT
* * **
61321843 AAAGGTTGCGATTTTAAATCGATGAACCTTAAATGAAAGTCCATATCTTAAATTGCTAACGCTAA
131 AAAGGTTGCAATCTTAAATCGA-GAACCTTAAATGAAAGTCCATATCTTAAATCACTAACGCTAA
* *
61321908 GATTCTGAAAATCCTTAAAGTTTGAAGGTTGCGATCTTAAATCAGTGAACCTTAAAGGAGAGTTG
195 GATTATCAAAATCCTTAAAGTTTGAAGGTTGCGATCTTAAATCAGTGAACCTTAAAGGAGAGTTG
61321973 CAATT
260 CAATT
* ** * *
61321978 TTAAATCGTTAAGTCTAAGATTCTAAAAATCCTTGAAGTTTG-AAGGTTGTGATCTTAAATTGGC
1 TTAAATCGCTAACACTAAAATTCTAAAAATCCTTGAAGTTTGAAAGGTTGTGATCTTAAATCGGC
* ** * * *
61322042 AAACCTTAAAGGGGACTCGTGATCTTAAACCTCTAACTCTAAGATTCT-AAATATTCTTGGATTT
66 AAACCTTAAAAGGGACTCACGATCTTAAACCGCTAACTCTAAGATTCTGAAA-ATCCTTGAATTT
* * * *
61322106 TGAAGGTTGCAATCTTAAATC-AGCAAACCTTAAA-GAGGAGT-CGTGATCTTAAATCACTAACT
130 TAAAGGTTGCAATCTTAAATCGAG--AACCTTAAATGA-AAGTCCAT-ATCTTAAATCACTAACG
* * * *
61322168 CTATGATTATCAAAATCTTTGAAGTTTGAAGGTTGTGATCTTAAAT
191 CTAAGATTATCAAAATCCTTAAAGTTTGAAGGTTGCGATCTTAAAT
61322214 AACAACTCAA
Statistics
Matches: 202, Mismatches: 29, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
262 1 0.00
263 8 0.04
264 156 0.77
265 37 0.18
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (264 bp):
TTAAATCGCTAACACTAAAATTCTAAAAATCCTTGAAGTTTGAAAGGTTGTGATCTTAAATCGGC
AAACCTTAAAAGGGACTCACGATCTTAAACCGCTAACTCTAAGATTCTGAAAATCCTTGAATTTT
AAAGGTTGCAATCTTAAATCGAGAACCTTAAATGAAAGTCCATATCTTAAATCACTAACGCTAAG
ATTATCAAAATCCTTAAAGTTTGAAGGTTGCGATCTTAAATCAGTGAACCTTAAAGGAGAGTTGC
AATT
Found at i:61338635 original size:3 final size:3
Alignment explanation
Indices: 61338627--61338659 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
61338617 ACCAAAATGT
61338627 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
61338660 TGAGAGTATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:61346902 original size:18 final size:18
Alignment explanation
Indices: 61346871--61346906 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
61346861 ATAATCTGTG
* *
61346871 ACAAGGGAATTACAATCA
1 ACAAGAGAACTACAATCA
61346889 ACAAGAGAACTACAATCA
1 ACAAGAGAACTACAATCA
61346907 GCATCCTCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.19, G:0.14, T:0.14
Consensus pattern (18 bp):
ACAAGAGAACTACAATCA
Found at i:61348505 original size:25 final size:24
Alignment explanation
Indices: 61348458--61348529 Score: 58
Period size: 25 Copynumber: 2.9 Consensus size: 24
61348448 AGCTTATCGT
** * *
61348458 TATTCAGCTCACATGAGCTTACCGA
1 TATTCAGCTCGTAAGAGCATACC-A
61348483 TATTCAGCTCGTAAGAGCATACCA
1 TATTCAGCTCGTAAGAGCATACCA
61348507 -ATTCAGAGCTCGTATA-AGCATAC
1 TATTC--AGCTCGTA-AGAGCATAC
61348530 ATGTACAGGA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
23 4 0.10
24 1 0.03
25 34 0.85
26 1 0.03
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (24 bp):
TATTCAGCTCGTAAGAGCATACCA
Found at i:61359926 original size:37 final size:37
Alignment explanation
Indices: 61359871--61359956 Score: 118
Period size: 37 Copynumber: 2.3 Consensus size: 37
61359861 TCAATGGCAT
* * *
61359871 GCTTATCATGCTTTCAGTTTAATAATTTTAGTAGCAG
1 GCTTATCATGCTTCCAGTTTAACAATTTCAGTAGCAG
* *
61359908 GCTTATCATGCTTCCAGTTTAACAATTTCAGTGGCAT
1 GCTTATCATGCTTCCAGTTTAACAATTTCAGTAGCAG
61359945 GCTTAATCATGC
1 GCTT-ATCATGC
61359957 ATTCATTAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
37 36 0.84
38 7 0.16
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.40
Consensus pattern (37 bp):
GCTTATCATGCTTCCAGTTTAACAATTTCAGTAGCAG
Found at i:61360581 original size:3 final size:3
Alignment explanation
Indices: 61360567--61360599 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
61360557 ATAATTCGGC
*
61360567 AAG AAG AA- AAG AAG AAG AAA AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
61360600 GAACACAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:61360609 original size:20 final size:20
Alignment explanation
Indices: 61360567--61360609 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
61360557 ATAATTCGGC
*
61360567 AAGAAGAAAAGAAGAAGAAA
1 AAGAAGAAAAGAAGAACAAA
*
61360587 AAGAAGAAGAAG-AGAACACA
1 AAGAAGAA-AAGAAGAACAAA
61360607 AAG
1 AAG
61360610 GGGCGACACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 17 0.85
21 3 0.15
ACGTcount: A:0.70, C:0.05, G:0.26, T:0.00
Consensus pattern (20 bp):
AAGAAGAAAAGAAGAACAAA
Found at i:61360677 original size:21 final size:21
Alignment explanation
Indices: 61360629--61360685 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 21
61360619 AAGGGTGAAA
* *
61360629 AGAAAATAAGGAAAGAAAATGGG
1 AGAAAAT-A-GAAGGAAAATGAG
61360652 AGAAAAT-GAAGGAAAATTGAG
1 AGAAAATAGAAGGAAAA-TGAG
61360673 AGAAAATAGAAGG
1 AGAAAATAGAAGG
61360686 GGATGGGACA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
20 8 0.27
21 10 0.33
22 5 0.17
23 7 0.23
ACGTcount: A:0.60, C:0.00, G:0.30, T:0.11
Consensus pattern (21 bp):
AGAAAATAGAAGGAAAATGAG
Found at i:61376680 original size:102 final size:101
Alignment explanation
Indices: 61376491--61376834 Score: 442
Period size: 102 Copynumber: 3.4 Consensus size: 101
61376481 TATCGATGAA
*
61376491 CACGTGTGTAGTACTATGTGAAGGCTACTACATGTATCGATAAATAATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACATGAATCGATAAATAATGGTCACATGTGTAGTAC
* * *
61376556 TAAGTGAATGCTACAATATGTACCGAGAAGCTTTGGT
66 TAAGTGAAGGCTACTATGTGTACCGA-AAGCTTTGGT
* * * *
61376593 TACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACATGAATCGATAAATAATGGTCACATGTGTAGTAC
* *
61376658 TAAGTGAAGGCTAGTATGTGTACTGAAAAGCTTTGGT
66 TAAGTGAAGGCTACTATGTGTACCG-AAAGCTTTGGT
* * * *
61376695 CACGTGTGTAGTACTATGTGAAGGCTATTACATGAACCG-TAAA-ACTTGATCACATGTGTAGTA
1 CACGTGTGTAGTACTATGTGAAGGCTACTACATGAATCGATAAATA-ATGGTCACATGTGTAGTA
* * * * *
61376758 CTATGTGAAGGCTACTACGTGAACCGTAAAAC-TTGAT
65 CTAAGTGAAGGCTACTATGTGTACCG-AAAGCTTTGGT
* *
61376795 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGA
1 CACGTGTGTAGTACTATGTGAAGGCTACTACATGAATCGA
61376835 ATGATAAAAG
Statistics
Matches: 209, Mismatches: 30, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
100 39 0.19
101 45 0.22
102 124 0.59
103 1 0.00
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (101 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACATGAATCGATAAATAATGGTCACATGTGTAGTAC
TAAGTGAAGGCTACTATGTGTACCGAAAGCTTTGGT
Found at i:61376826 original size:50 final size:50
Alignment explanation
Indices: 61376491--61376828 Score: 331
Period size: 51 Copynumber: 6.7 Consensus size: 50
61376481 TATCGATGAA
* * * *
61376491 CACGTGTGTAGTACTATGTGAAGGCTACTACATGTATCGATAAATA-ATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCG-TAAA-ACTTGGT
* * * * ** * *
61376542 CACATGTGTAGTACTAAGTGAATGCTACAATATGTACCG-AGAAGCTTTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTA-AAAC-TTGGT
* * * ***
61376593 TACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCG-TAAAACTTGGT
* * * * * *
61376644 CACATGTGTAGTACTAAGTGAAGGCTAGTATGTGTACTG-AAAAGCTTTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAA-C-TTGGT
* * *
61376695 CACGTGTGTAGTACTATGTGAAGGCTATTACATGAACCGTAAAACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGGT
* *
61376745 CACATGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGGT
61376795 CACGTGTGTAGTACTATGTGAAGGCTACTACGTG
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTG
61376829 TATCGAATGA
Statistics
Matches: 234, Mismatches: 45, Indels: 17
0.79 0.15 0.06
Matches are distributed among these distances:
49 4 0.02
50 86 0.37
51 137 0.59
52 6 0.03
53 1 0.00
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (50 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGGT
Found at i:61379618 original size:21 final size:21
Alignment explanation
Indices: 61379594--61379641 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
61379584 TAGTTAGCGT
*
61379594 ACACGGGCATATGAAGTAGTC
1 ACACGGGCATATGAAGTAGCC
* *
61379615 ACACGGGCGTGTGAAGTAGCC
1 ACACGGGCATATGAAGTAGCC
61379636 ACACGG
1 ACACGG
61379642 CCATGTCTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.29, C:0.23, G:0.33, T:0.15
Consensus pattern (21 bp):
ACACGGGCATATGAAGTAGCC
Found at i:61380231 original size:33 final size:33
Alignment explanation
Indices: 61380189--61380255 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
61380179 GAAATAAATA
61380189 AAAATAAAAATATTTAATTAACTAAAAAAATTC
1 AAAATAAAAATATTTAATTAACTAAAAAAATTC
**
61380222 AAAATAAAAATATTTAATTATGTAAAAAAATTC
1 AAAATAAAAATATTTAATTAACTAAAAAAATTC
61380255 A
1 A
61380256 CACCAAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.63, C:0.04, G:0.01, T:0.31
Consensus pattern (33 bp):
AAAATAAAAATATTTAATTAACTAAAAAAATTC
Found at i:61380264 original size:33 final size:33
Alignment explanation
Indices: 61380189--61380264 Score: 98
Period size: 33 Copynumber: 2.3 Consensus size: 33
61380179 GAAATAAATA
*
61380189 AAAATAAAAATATTTAATTAACTAAAAAAATTC
1 AAAACAAAAATATTTAATTAACTAAAAAAATTC
* **
61380222 AAAATAAAAATATTTAATTATGTAAAAAAATTC
1 AAAACAAAAATATTTAATTAACTAAAAAAATTC
* *
61380255 ACACCAAAAA
1 AAAACAAAAA
61380265 AATAATAATA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.63, C:0.08, G:0.01, T:0.28
Consensus pattern (33 bp):
AAAACAAAAATATTTAATTAACTAAAAAAATTC
Found at i:61384129 original size:21 final size:21
Alignment explanation
Indices: 61384103--61384152 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
61384093 GATACTTATG
*
61384103 CAAGTATCGTTACCTTTCTAA
1 CAAGTATCGATACCTTTCTAA
*
61384124 CAAGTATCGATATCTTTCTAA
1 CAAGTATCGATACCTTTCTAA
*
61384145 AAAGTATC
1 CAAGTATC
61384153 AACACTTTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.34, C:0.20, G:0.10, T:0.36
Consensus pattern (21 bp):
CAAGTATCGATACCTTTCTAA
Found at i:61390102 original size:3 final size:3
Alignment explanation
Indices: 61390094--61390128 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
61390084 AAAATTGCAA
61390094 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
61390129 GAGGACTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:61390251 original size:14 final size:14
Alignment explanation
Indices: 61390232--61390261 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
61390222 AACTGATGGC
61390232 TTTTAATTTTAGGT
1 TTTTAATTTTAGGT
61390246 TTTTAATTTTAGGT
1 TTTTAATTTTAGGT
61390260 TT
1 TT
61390262 ATATAGTGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.20, C:0.00, G:0.13, T:0.67
Consensus pattern (14 bp):
TTTTAATTTTAGGT
Found at i:61390316 original size:19 final size:18
Alignment explanation
Indices: 61390280--61390321 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
61390270 TAATTAATTT
61390280 ATTAATTAACTAATATTA
1 ATTAATTAACTAATATTA
*
61390298 ACTTAATTAACCTTA-ATTA
1 A-TTAATTAA-CTAATATTA
61390317 ATTAA
1 ATTAA
61390322 CACTAAACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 5 0.24
19 13 0.62
20 3 0.14
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.43
Consensus pattern (18 bp):
ATTAATTAACTAATATTA
Found at i:61393220 original size:18 final size:19
Alignment explanation
Indices: 61393193--61393228 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
61393183 GAACATCGAA
61393193 GAAATAG-AAAAGAAAAAT
1 GAAATAGAAAAAGAAAAAT
*
61393211 GAAATCGAAAAAGAAAAA
1 GAAATAGAAAAAGAAAAA
61393229 AATCAGATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.72, C:0.03, G:0.17, T:0.08
Consensus pattern (19 bp):
GAAATAGAAAAAGAAAAAT
Found at i:61394142 original size:44 final size:42
Alignment explanation
Indices: 61394087--61394271 Score: 142
Period size: 44 Copynumber: 4.3 Consensus size: 42
61394077 GATCTATTTT
* *
61394087 ACTGGAACTTCAGAGAGATAAGATCTATCATTTTAATCCGCTCC
1 ACTGCAACTTCAGAGAGATAAGATCT-TCA-TTTAATCTGCTCC
* * * *
61394131 ACTGCAACTTCAGGGAGATAAGATTGGTTCATTCAGTCTGC-CC
1 ACTGCAACTTCAGAGAGATAAGA-T-CTTCATTTAATCTGCTCC
* * * * *
61394174 TACTGCAACTTCAGGGAGATAAGA-CTTGATGTGATTTGCT-C
1 -ACTGCAACTTCAGAGAGATAAGATCTTCATTTAATCTGCTCC
* ** *
61394215 TCTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATTTGCTCC
1 ACTGCAACTTCAGAGAGATAAGATCT-T-CATTTAATCTGCTCC
*
61394259 ACTGTAACTTCAG
1 ACTGCAACTTCAG
61394272 GAAGATAGGA
Statistics
Matches: 113, Mismatches: 20, Indels: 16
0.76 0.13 0.11
Matches are distributed among these distances:
40 21 0.19
41 11 0.10
42 1 0.01
43 12 0.11
44 63 0.56
45 4 0.04
46 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.31
Consensus pattern (42 bp):
ACTGCAACTTCAGAGAGATAAGATCTTCATTTAATCTGCTCC
Found at i:61394268 original size:128 final size:128
Alignment explanation
Indices: 61394092--61394325 Score: 319
Period size: 128 Copynumber: 1.8 Consensus size: 128
61394082 ATTTTACTGG
*
61394092 AACTTCAGAGAGATAAGATCTATCATTTTAATCCGCTCCACTGCAACTTCAGGGAGATAAGATT-
1 AACTTCAGAGAGATAAGATCTATCATTTTAATCCGCTCCACTGCAACTTCAGGAAGATAAGATTA
* * *
61394156 GGTTCATTCAGTCTGC-CCTACTGCAACTTCAGGGAGATAAGACTTGATGTGATTTGCTCTCTGC
66 GGTTC-TTCAATCTGCTCC-ACTACAACTTCAGGGAAATAAGACTTGATGTGATTTGCTCTCTGC
* ** ** * *
61394220 AACTTCAGAGAGATAAGATCTGTGGTTTTAATTTGCTCCACTGTAACTTCAGGAAGATAGGATTA
1 AACTTCAGAGAGATAAGATCTATCATTTTAATCCGCTCCACTGCAACTTCAGGAAGATAAGATTA
* *
61394285 GTTTCTTCAATCTGCTCCATTACAACTTCAGGGAAATAAGA
66 GGTTCTTCAATCTGCTCCACTACAACTTCAGGGAAATAAGA
61394326 TTCGCCATCT
Statistics
Matches: 91, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
128 85 0.93
129 6 0.07
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (128 bp):
AACTTCAGAGAGATAAGATCTATCATTTTAATCCGCTCCACTGCAACTTCAGGAAGATAAGATTA
GGTTCTTCAATCTGCTCCACTACAACTTCAGGGAAATAAGACTTGATGTGATTTGCTCTCTGC
Found at i:61394278 original size:44 final size:42
Alignment explanation
Indices: 61394117--61394325 Score: 135
Period size: 44 Copynumber: 4.9 Consensus size: 42
61394107 AGATCTATCA
* *
61394117 TTTTAATCCGCTCCACTGCAACTTCAGGGAGATAAGA-TTGG
1 TTTTAATCTGCTCCACTGCAACTTCAGGAAGATAAGACTTGG
* *
61394158 TTCATTCAGTCTGC-CCTACTGCAACTTCAGGGAGATAAGACTT-G
1 TT--TT-AATCTGCTCC-ACTGCAACTTCAGGAAGATAAGACTTGG
* * * * *
61394202 ATGTGATTTGCT-CTCTGCAACTTCA-GAGAGATAAGATCTGTGG
1 TTTTAATCTGCTCCACTGCAACTTCAGGA-AGATAAGA-CT-TGG
* * * *
61394245 TTTTAATTTGCTCCACTGTAACTTCAGGAAGATAGGA-TTAGT
1 TTTTAATCTGCTCCACTGCAACTTCAGGAAGATAAGACTT-GG
* *
61394287 TTCTTCAATCTGCTCCATTACAACTTCAGGGAA-ATAAGA
1 TT-TT-AATCTGCTCCACTGCAACTTCA-GGAAGATAAGA
61394326 TTCGCCATCT
Statistics
Matches: 131, Mismatches: 21, Indels: 29
0.72 0.12 0.16
Matches are distributed among these distances:
39 1 0.01
40 19 0.15
41 10 0.08
42 6 0.05
43 16 0.12
44 71 0.54
45 8 0.06
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (42 bp):
TTTTAATCTGCTCCACTGCAACTTCAGGAAGATAAGACTTGG
Found at i:61394811 original size:24 final size:24
Alignment explanation
Indices: 61394779--61394830 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
61394769 CCGGATTGCC
*
61394779 TCCACTGTAATCTTCAAGGTTCAA
1 TCCACTGTAATCTTCAAGGTCCAA
61394803 TCCACTGTAATCTTCAAGGTCCAA
1 TCCACTGTAATCTTCAAGGTCCAA
61394827 TCCA
1 TCCA
61394831 TTGTGCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.29, C:0.29, G:0.12, T:0.31
Consensus pattern (24 bp):
TCCACTGTAATCTTCAAGGTCCAA
Found at i:61399203 original size:38 final size:38
Alignment explanation
Indices: 61399156--61399232 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
61399146 CGGAGATAGG
61399156 TTATGATCTATGTTATCTTCAAAGTCATGAGATCCCTC
1 TTATGATCTATGTTATCTTCAAAGTCATGAGATCCCTC
61399194 TTATGATCTATGTTATCTTCAAAGTCATGAGATCCCTC
1 TTATGATCTATGTTATCTTCAAAGTCATGAGATCCCTC
61399232 T
1 T
61399233 AAACACATGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.40
Consensus pattern (38 bp):
TTATGATCTATGTTATCTTCAAAGTCATGAGATCCCTC
Found at i:61403543 original size:13 final size:13
Alignment explanation
Indices: 61403525--61403556 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
61403515 TAACTCTTCT
61403525 ATTCTTTTTTTCA
1 ATTCTTTTTTTCA
61403538 ATTCTTTTTTTCA
1 ATTCTTTTTTTCA
61403551 ATTCTT
1 ATTCTT
61403557 CAATCCTGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.69
Consensus pattern (13 bp):
ATTCTTTTTTTCA
Found at i:61407785 original size:130 final size:130
Alignment explanation
Indices: 61407552--61407812 Score: 488
Period size: 130 Copynumber: 2.0 Consensus size: 130
61407542 GACAAATAAA
*
61407552 ACGCAATGGGATAATAATGTACAATGTGAAGTGATAATTCGTAAACTAAAATGTACACTAGTGAT
1 ACGCAATGGGATAATAATGTACAATGTGAAATGATAATTCGTAAACTAAAATGTACACTAGTGAT
61407617 CGACAAATAATCCATAAATACTAATAAACAAAACAATACACATGAGAGCAACAATCCTACATGAT
66 CGACAAATAATCCATAAATACTAATAAACAAAACAATACACATGAGAGCAACAATCCTACATGAT
61407682 ACGCAATGGGATAATAATGTACAATGTGAAATGATAATTCGTAAACTAAAATGTACACTAGTGAT
1 ACGCAATGGGATAATAATGTACAATGTGAAATGATAATTCGTAAACTAAAATGTACACTAGTGAT
*
61407747 CGGCAAATAATCCATAAATAC-AAGTAAACAAAACAATACACATGAGAGCAACAATCCTACATGA
66 CGACAAATAATCCATAAATACTAA-TAAACAAAACAATACACATGAGAGCAACAATCCTACATGA
61407811 T
130 T
61407812 A
1 A
61407813 TATTATGCAA
Statistics
Matches: 128, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
129 2 0.02
130 126 0.98
ACGTcount: A:0.47, C:0.16, G:0.14, T:0.23
Consensus pattern (130 bp):
ACGCAATGGGATAATAATGTACAATGTGAAATGATAATTCGTAAACTAAAATGTACACTAGTGAT
CGACAAATAATCCATAAATACTAATAAACAAAACAATACACATGAGAGCAACAATCCTACATGAT
Found at i:61410791 original size:24 final size:22
Alignment explanation
Indices: 61410747--61410849 Score: 75
Period size: 24 Copynumber: 4.5 Consensus size: 22
61410737 AATGATGAAT
* *
61410747 TTAAAATAATAATGTTGATAAA
1 TTAAAATAATAATGATAATAAA
61410769 TTATAAATAATAATGCATAATAAA
1 TTA-AAATAATAATG-ATAATAAA
*
61410793 TCTAAGATAATAAAAT-ATAATAAA
1 T-TAAAATAAT--AATGATAATAAA
* * *
61410817 TT-AAACAATATTAATAATAAAA
1 TTAAAATAATAATGATAAT-AAA
*
61410839 CTAAAATAATA
1 TTAAAATAATA
61410850 TTAAGTTTAA
Statistics
Matches: 65, Mismatches: 8, Indels: 15
0.74 0.09 0.17
Matches are distributed among these distances:
20 2 0.03
21 5 0.08
22 12 0.18
23 19 0.29
24 22 0.34
25 2 0.03
26 3 0.05
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.32
Consensus pattern (22 bp):
TTAAAATAATAATGATAATAAA
Found at i:61411149 original size:17 final size:18
Alignment explanation
Indices: 61411117--61411150 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
61411107 GAAACAGAAA
*
61411117 TAAAATGGAGATAAAATT
1 TAAAATGGAAATAAAATT
61411135 TAAAA-GGAAATAAAAT
1 TAAAATGGAAATAAAAT
61411151 ACAAAAAGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.62, C:0.00, G:0.15, T:0.24
Consensus pattern (18 bp):
TAAAATGGAAATAAAATT
Found at i:61416874 original size:24 final size:24
Alignment explanation
Indices: 61416847--61416908 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 24
61416837 ATTTTTAAAT
61416847 TAAAATTTAATTAAAATATATATA
1 TAAAATTTAATTAAAATATATATA
* * * *
61416871 TAAAATAGTAACT-AAATATATTTT
1 TAAAAT-TTAATTAAAATATATATA
*
61416895 TAAAATTTTATTAA
1 TAAAATTTAATTAA
61416909 TTTTTGAATA
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
23 3 0.10
24 22 0.76
25 4 0.14
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (24 bp):
TAAAATTTAATTAAAATATATATA
Found at i:61425431 original size:110 final size:112
Alignment explanation
Indices: 61425237--61425549 Score: 342
Period size: 110 Copynumber: 2.8 Consensus size: 112
61425227 CAGTATGACC
* * * *
61425237 GAAGTACAAATTGTGCCCAACACTCATCGATACGTAGTCGAAGTAATCATTTGGCACCCAGTGCC
1 GAAGTAAAAATTGTGTCCAGCACTCATCGACACGTAGTCGAAGTAATCATTTGGCACCCAGTGCC
* * * * * * *
61425302 TCATTGGAATGTTCAAAGTAATTAATTTGCGCCCAACGC-TC-AATT
66 TCATCGGAACGTCCGAAGTAAGTAATTTGCACCCAACGCTTCGAACT
* * * *
61425347 GAAGTAAAAATTGTGTCTAGCACTCATTGACACATAGTCGAAGTAATCATTTGACACCCAGTGCC
1 GAAGTAAAAATTGTGTCCAGCACTCATCGACACGTAGTCGAAGTAATCATTTGGCACCCAGTGCC
* * * *
61425412 TCATCGGAACCTCCGAAGTAAGTAGTTTGCACCCAATGCTTATCGGTTGACT
66 TCATCGGAACGTCCGAAGTAAGTAATTTGCACCCAACGC-T-TC-G--AACT
* ** * *
61425464 GAAGTAAAAATTATGTCCAGCACTCAGGGGCACGTAGTCGAAGTAATCATTTGGCACCCAGTACC
1 GAAGTAAAAATTGTGTCCAGCACTCATCGACACGTAGTCGAAGTAATCATTTGGCACCCAGTGCC
*
61425529 TCATCGAAACGTCCGAAGTAA
66 TCATCGGAACGTCCGAAGTAA
61425550 AGTGCACCCA
Statistics
Matches: 167, Mismatches: 29, Indels: 7
0.82 0.14 0.03
Matches are distributed among these distances:
110 87 0.52
113 2 0.01
117 78 0.47
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (112 bp):
GAAGTAAAAATTGTGTCCAGCACTCATCGACACGTAGTCGAAGTAATCATTTGGCACCCAGTGCC
TCATCGGAACGTCCGAAGTAAGTAATTTGCACCCAACGCTTCGAACT
Found at i:61425509 original size:117 final size:113
Alignment explanation
Indices: 61425346--61425564 Score: 312
Period size: 117 Copynumber: 1.9 Consensus size: 113
61425336 AACGCTCAAT
* * ** *
61425346 TGAAGTAAAAATTGTGTCTAGCACTCATTGACACATAGTCGAAGTAATCATTTGACACCCAGTGC
1 TGAAGTAAAAATTATGTCCAGCACTCAGGGACACATAGTCGAAGTAATCATTTGACACCCAGTAC
*
61425411 CTCATCGGAACCTCCGAAGTAAGTAGTTTGCACCCAATGCTTATCGGTTGAC
66 CTCATCGAAACCTCCGAAGTAA--AG--TGCACCCAATGCTTATCGGTTGAC
* * *
61425463 TGAAGTAAAAATTATGTCCAGCACTCAGGGGCACGTAGTCGAAGTAATCATTTGGCACCCAGTAC
1 TGAAGTAAAAATTATGTCCAGCACTCAGGGACACATAGTCGAAGTAATCATTTGACACCCAGTAC
*
61425528 CTCATCGAAACGTCCGAAGTAAAGTGCACCCAATGCT
66 CTCATCGAAACCTCCGAAGTAAAGTGCACCCAATGCT
61425565 CATTGACATA
Statistics
Matches: 92, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
113 13 0.14
115 2 0.02
117 77 0.84
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.25
Consensus pattern (113 bp):
TGAAGTAAAAATTATGTCCAGCACTCAGGGACACATAGTCGAAGTAATCATTTGACACCCAGTAC
CTCATCGAAACCTCCGAAGTAAAGTGCACCCAATGCTTATCGGTTGAC
Found at i:61431825 original size:19 final size:19
Alignment explanation
Indices: 61431790--61431828 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
61431780 CGACGCCGAT
61431790 TCTGTAAGTGTTCTAAAAA
1 TCTGTAAGTGTTCTAAAAA
*
61431809 TCTGATAAGT-TTTTAAAAA
1 TCTG-TAAGTGTTCTAAAAA
61431828 T
1 T
61431829 ATGAGTAGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.38, C:0.08, G:0.13, T:0.41
Consensus pattern (19 bp):
TCTGTAAGTGTTCTAAAAA
Found at i:61432106 original size:20 final size:20
Alignment explanation
Indices: 61432062--61432107 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
61432052 CCGCTAGAAA
*
61432062 ATAAAAAAAACAAATAAACC
1 ATAAAAAAAACAAATAAAAC
*
61432082 A-AAAAAAAACAAA-ACAAAG
1 ATAAAAAAAACAAATA-AAAC
61432101 ATAAAAA
1 ATAAAAA
61432108 TTAATAGTCC
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 1 0.05
19 15 0.68
20 6 0.27
ACGTcount: A:0.80, C:0.11, G:0.02, T:0.07
Consensus pattern (20 bp):
ATAAAAAAAACAAATAAAAC
Found at i:61435602 original size:51 final size:51
Alignment explanation
Indices: 61435504--61435829 Score: 221
Period size: 51 Copynumber: 6.3 Consensus size: 51
61435494 ACTTCTGATC
* * *
61435504 AGTGACAAGTGATAAGTGGTAG-TTTAGTTACAGTTATCTGATCAGTGATA
1 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
61435554 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
* * * *
61435605 AGTGACAAGTGATAAAT-GTGATCCGTGTAAGGCCATGGCAGGGC-TATGGCT--TC-G-GA-A
1 AGTGACAAGTGATAAGTGGT-A-GC-T-TTA-G-C-T-ACA---CTTAT--CTGATCAGTGACA
* * * * * * * * *
61435662 AATG-CTAAGTGATCATACGTAAG-AGCACTTATCT-GA-TCA-GTGATAAGTGATA
1 AGTGAC-AAGTGAT-A-A-GT-GGTAGC-TTTAGCTACACTTATCTGATCAGTGACA
*
61435714 AGTGACAAGTGATAAGTGGTAGC-TTAGCTACACTTATCTGATCGGTGACA
1 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
*
61435764 AGTGACAATTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
61435815 AGTGACAAGTGATAA
1 AGTGACAAGTGATAA
61435830 ATGTGATCCG
Statistics
Matches: 214, Mismatches: 30, Indels: 63
0.70 0.10 0.21
Matches are distributed among these distances:
47 6 0.03
48 2 0.01
49 8 0.04
50 58 0.27
51 85 0.40
52 12 0.06
53 3 0.01
54 2 0.01
55 2 0.01
56 3 0.01
57 12 0.06
58 7 0.03
59 3 0.01
60 7 0.03
61 1 0.00
62 3 0.01
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.29
Consensus pattern (51 bp):
AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
Found at i:61435710 original size:7 final size:7
Alignment explanation
Indices: 61435695--61435731 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
61435685 AGCACTTATC
*
61435695 TGATCAG
1 TGATAAG
61435702 TGATAAG
1 TGATAAG
61435709 TGATAAG
1 TGATAAG
*
61435716 TGACAAG
1 TGATAAG
61435723 TGATAAG
1 TGATAAG
61435730 TG
1 TG
61435732 GTAGCTTAGC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.38, C:0.05, G:0.30, T:0.27
Consensus pattern (7 bp):
TGATAAG
Found at i:61435866 original size:210 final size:210
Alignment explanation
Indices: 61435499--61435895 Score: 731
Period size: 210 Copynumber: 1.9 Consensus size: 210
61435489 TGAATACTTC
* * * * *
61435499 TGATCAGTGACAAGTGATAAGTGGTAGTTTAGTTACAGTTATCTGATCAGTGATAAGTGACAAGT
1 TGATAAGTGACAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAGTGACAAGTGACAAGT
61435564 GATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGACAAGTGATAAATGTGATCC
66 GATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGACAAGTGATAAATGTGATCC
61435629 GTGTAAGGCCATGGCAGGGCTATGGCTTCGGAAAATGCTAAGTGATCATACGTAAGAGCACTTAT
131 GTGTAAGGCCATGGCAGGGCTATGGCTTCGGAAAATGCTAAGTGATCATACGTAAGAGCACTTAT
61435694 CTGATCAGTGATAAG
196 CTGATCAGTGATAAG
* *
61435709 TGATAAGTGACAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCGGTGACAAGTGACAATT
1 TGATAAGTGACAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAGTGACAAGTGACAAGT
61435774 GATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGACAAGTGATAAATGTGATCC
66 GATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGACAAGTGATAAATGTGATCC
61435839 GTGTAAGGCCATGGCAGGGCTATGGCTTCGGAAAATGCTAAGTGATCATACGTAAGA
131 GTGTAAGGCCATGGCAGGGCTATGGCTTCGGAAAATGCTAAGTGATCATACGTAAGA
61435896 CCATAATTAT
Statistics
Matches: 180, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
210 180 1.00
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.28
Consensus pattern (210 bp):
TGATAAGTGACAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAGTGACAAGTGACAAGT
GATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGACAAGTGATAAATGTGATCC
GTGTAAGGCCATGGCAGGGCTATGGCTTCGGAAAATGCTAAGTGATCATACGTAAGAGCACTTAT
CTGATCAGTGATAAG
Found at i:61436645 original size:57 final size:59
Alignment explanation
Indices: 61436553--61436672 Score: 172
Period size: 57 Copynumber: 2.1 Consensus size: 59
61436543 TTATTTCCGA
* * * *
61436553 TTCTCCCCAATTTTTTTTTCTTTTAAAAGTTCGATTTGGCCCCCTTTTTTGTTTTGTTT
1 TTCTCCCCAATTTGTTTTTCGTTGAAAAGTTCGATTTGGCCCACTTTTTTGTTTTGTTT
* *
61436612 TTCTCCCCAA-TTGTTTTT-GTTGAAAAGTTCGATTTGGCCCATTTTTTTGTTTTTTTT
1 TTCTCCCCAATTTGTTTTTCGTTGAAAAGTTCGATTTGGCCCACTTTTTTGTTTTGTTT
61436669 TTCT
1 TTCT
61436673 GCTCTTTTTG
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
57 38 0.69
58 7 0.13
59 10 0.18
ACGTcount: A:0.12, C:0.18, G:0.12, T:0.57
Consensus pattern (59 bp):
TTCTCCCCAATTTGTTTTTCGTTGAAAAGTTCGATTTGGCCCACTTTTTTGTTTTGTTT
Found at i:61436861 original size:80 final size:81
Alignment explanation
Indices: 61436689--61436871 Score: 201
Period size: 80 Copynumber: 2.3 Consensus size: 81
61436679 TTTGCTATTT
*
61436689 TATTACTAAATTAATTAATTTAACATTATTGTTACTATCATTATATTTTCTTTTTTATTTTACTA
1 TATTACTAAATTAATTAATTTAACATTATTATTACTATCA-TATATTTTCTTTTTTATTTTACTA
*
61436754 ACTTATTAGTATCATTA
65 ACTTATTAGTATCATCA
* * * * * *
61436771 TATTATTAAATTAATTAGTTTAATATTGTTATTACTA-C-TATCATTTTCTTTTTTA-TTTATTT
1 TATTACTAAATTAATTAATTTAACATTATTATTACTATCATAT-ATTTTCTTTTTTATTTTACTA
* * *
61436833 ATTTACTTATTATTATCA
65 ACTTA-TTAGTATCATCA
* *
61436851 TATTACTAAATCAATCAATTT
1 TATTACTAAATTAATTAATTT
61436872 TGCTTATTTC
Statistics
Matches: 84, Mismatches: 15, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
79 12 0.14
80 39 0.46
81 1 0.01
82 32 0.38
ACGTcount: A:0.33, C:0.09, G:0.02, T:0.56
Consensus pattern (81 bp):
TATTACTAAATTAATTAATTTAACATTATTATTACTATCATATATTTTCTTTTTTATTTTACTAA
CTTATTAGTATCATCA
Found at i:61436951 original size:20 final size:19
Alignment explanation
Indices: 61436914--61436954 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
61436904 TTTATCTAAA
61436914 ATTTTTCATATATACATTT
1 ATTTTTCATATATACATTT
* *
61436933 ATTTTATCATTTATTCATTT
1 ATTTT-TCATATATACATTT
61436953 AT
1 AT
61436955 GTCCTTTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.29, C:0.10, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTTTTCATATATACATTT
Found at i:61441534 original size:80 final size:81
Alignment explanation
Indices: 61441362--61441544 Score: 201
Period size: 80 Copynumber: 2.3 Consensus size: 81
61441352 TTTGCTATTT
*
61441362 TATTACTAAATTAATTAATTTAACATTATTGTTACTATCATTATATTTTCTTTTTTATTTTACTA
1 TATTACTAAATTAATTAATTTAACATTATTATTACTATCA-TATATTTTCTTTTTTATTTTACTA
* *
61441427 ACTTATTAGTATCATTA
65 ACTTATTACTATCATCA
* * * * * *
61441444 TATTATTAAATTAATTAGTTTAATATTGTTATTACTA-C-TATCATTTTCTTTTTTA-TTTATTT
1 TATTACTAAATTAATTAATTTAACATTATTATTACTATCATAT-ATTTTCTTTTTTATTTTACTA
* *
61441506 ATTTACTTACTATTATCA
65 ACTTA-TTACTATCATCA
* *
61441524 TATTACTAAATCAATCAATTT
1 TATTACTAAATTAATTAATTT
61441545 TGCGTTATTT
Statistics
Matches: 84, Mismatches: 15, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
79 12 0.14
80 39 0.46
81 1 0.01
82 32 0.38
ACGTcount: A:0.33, C:0.10, G:0.02, T:0.55
Consensus pattern (81 bp):
TATTACTAAATTAATTAATTTAACATTATTATTACTATCATATATTTTCTTTTTTATTTTACTAA
CTTATTACTATCATCA
Found at i:61471147 original size:41 final size:42
Alignment explanation
Indices: 61471045--61471214 Score: 128
Period size: 48 Copynumber: 3.9 Consensus size: 42
61471035 CTATGTCCCA
61471045 AATATGGTCTTACATA-GAAATCTCATATCGATGCCAATAGCCC
1 AATATGGTCTT--ATACGAAATCTCATATCGATGCCAATAGCCC
* * * * *
61471088 AACTATGGTCTTACACGAAGTCTCATATCGATGTC-ATATCCT
1 AA-TATGGTCTTATACGAAATCTCATATCGATGCCAATAGCCC
* * * * *
61471130 TATATGGTCTTATACGAAATCCCAAATCAATGCCAATGTCATATCCC
1 AATATGGTCTTATACGAAATCTCATATCGATGCC-A----ATAGCCC
** *
61471177 AGATATGGTCTTATACGGTATCTCAAATCGATGCCAAT
1 A-ATATGGTCTTATACGAAATCTCATATCGATGCCAAT
61471215 GCCATATCCC
Statistics
Matches: 100, Mismatches: 18, Indels: 18
0.74 0.13 0.13
Matches are distributed among these distances:
41 26 0.26
42 8 0.08
43 21 0.21
44 9 0.09
47 7 0.07
48 29 0.29
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.31
Consensus pattern (42 bp):
AATATGGTCTTATACGAAATCTCATATCGATGCCAATAGCCC
Found at i:61471189 original size:48 final size:48
Alignment explanation
Indices: 61471118--61471241 Score: 178
Period size: 48 Copynumber: 2.6 Consensus size: 48
61471108 TCTCATATCG
**
61471118 ATGTCATAT-CCTTATATGGTCTTATACGAAATCCCAAATCAATGCCA
1 ATGTCATATCCCAGATATGGTCTTATACGAAATCCCAAATCAATGCCA
** * *
61471165 ATGTCATATCCCAGATATGGTCTTATACGGTATCTCAAATCGATGCCA
1 ATGTCATATCCCAGATATGGTCTTATACGAAATCCCAAATCAATGCCA
*
61471213 ATGCCATATCCCAGATATGGTCTTATACG
1 ATGTCATATCCCAGATATGGTCTTATACG
61471242 GGATTTCAAA
Statistics
Matches: 69, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
47 9 0.13
48 60 0.87
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (48 bp):
ATGTCATATCCCAGATATGGTCTTATACGAAATCCCAAATCAATGCCA
Found at i:61471242 original size:48 final size:48
Alignment explanation
Indices: 61471131--61471256 Score: 189
Period size: 48 Copynumber: 2.6 Consensus size: 48
61471121 TCATATCCTT
* * *
61471131 ATATGGTCTTATACGAAATCCCAAATCAATGCCAATGTCATATCCCAG
1 ATATGGTCTTATACGGAATCTCAAATCAATGCCAATGCCATATCCCAG
* *
61471179 ATATGGTCTTATACGGTATCTCAAATCGATGCCAATGCCATATCCCAG
1 ATATGGTCTTATACGGAATCTCAAATCAATGCCAATGCCATATCCCAG
* *
61471227 ATATGGTCTTATACGGGATTTCAAATCAAT
1 ATATGGTCTTATACGGAATCTCAAATCAAT
61471257 TCGACAATAT
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 70 1.00
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (48 bp):
ATATGGTCTTATACGGAATCTCAAATCAATGCCAATGCCATATCCCAG
Found at i:61471282 original size:30 final size:30
Alignment explanation
Indices: 61471248--61471342 Score: 93
Period size: 32 Copynumber: 3.1 Consensus size: 30
61471238 TACGGGATTT
61471248 CAAATCAATTCGACAATATATATACATATA
1 CAAATCAATTCGACAATATATATACATATA
* * *
61471278 CAAATCATTTC-AGCAATGTATATATCTACATA
1 CAAATCAATTCGA-CAATATATATA-C-ATATA
* * *
61471310 TAAATCAATTCGGCAATATATAAAACATATA
1 CAAATCAATTCGACAATATAT-ATACATATA
61471341 CA
1 CA
61471343 TTTTAATTCA
Statistics
Matches: 50, Mismatches: 10, Indels: 9
0.72 0.14 0.13
Matches are distributed among these distances:
29 1 0.02
30 20 0.40
31 6 0.12
32 21 0.42
33 2 0.04
ACGTcount: A:0.47, C:0.17, G:0.05, T:0.31
Consensus pattern (30 bp):
CAAATCAATTCGACAATATATATACATATA
Found at i:61471300 original size:32 final size:32
Alignment explanation
Indices: 61471248--61471342 Score: 85
Period size: 30 Copynumber: 3.1 Consensus size: 32
61471238 TACGGGATTT
61471248 CAAATCAATTC-G-ACA-ATATATATACATATA
1 CAAATCAATTCAGCA-ATATATATATACATATA
* *
61471278 CAAATCATTTCAGCAATGTATATATCTACATAT-
1 CAAATCAATTCAGCAA--TATATATATACATATA
* *
61471311 -AAATCAATTCGGCAATATATA-AAACATATA
1 CAAATCAATTCAGCAATATATATATACATATA
61471341 CA
1 CA
61471343 TTTTAATTCA
Statistics
Matches: 52, Mismatches: 6, Indels: 13
0.73 0.08 0.18
Matches are distributed among these distances:
29 6 0.12
30 16 0.31
31 3 0.06
32 14 0.27
34 13 0.25
ACGTcount: A:0.47, C:0.17, G:0.05, T:0.31
Consensus pattern (32 bp):
CAAATCAATTCAGCAATATATATATACATATA
Found at i:61477705 original size:14 final size:14
Alignment explanation
Indices: 61477686--61477715 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
61477676 ATTGGTTTGG
61477686 TTGTTTGCCTGTAA
1 TTGTTTGCCTGTAA
*
61477700 TTGTTTGGCTGTAA
1 TTGTTTGCCTGTAA
61477714 TT
1 TT
61477716 TGCATTTCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.13, C:0.10, G:0.23, T:0.53
Consensus pattern (14 bp):
TTGTTTGCCTGTAA
Found at i:61482760 original size:51 final size:49
Alignment explanation
Indices: 61482702--61482888 Score: 178
Period size: 51 Copynumber: 3.7 Consensus size: 49
61482692 TCGGTTCACA
*
61482702 TAGTAGCCTACACATAGTACTACACATGTGACCATTACCATTCGATACACG
1 TAGTAGCCTACACATAGTACTACACACGTGACCA-TACCATTCG-TACACG
** ** * * * * * *
61482753 TAGTAGCCTGTACATAGTACTACTTACGTGATCGAAACTATCCGGTACGCA
1 TAGTAGCCTACACATAGTACTACACACGTGA-CCATACCATTC-GTACACG
* * * *
61482804 TAGTAGCCTGCACATAGTACTACACATGCGACC-TATCATTCTTGTACACG
1 TAGTAGCCTACACATAGTACTACACACGTGACCATACCATTC--GTACACG
61482854 TAGTAGCCTACACATAGTACTACACACGTGACCAT
1 TAGTAGCCTACACATAGTACTACACACGTGACCAT
61482889 CACTTTCACT
Statistics
Matches: 105, Mismatches: 27, Indels: 8
0.75 0.19 0.06
Matches are distributed among these distances:
49 4 0.04
50 36 0.34
51 62 0.59
52 3 0.03
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.26
Consensus pattern (49 bp):
TAGTAGCCTACACATAGTACTACACACGTGACCATACCATTCGTACACG
Found at i:61482907 original size:101 final size:101
Alignment explanation
Indices: 61482693--61482918 Score: 253
Period size: 101 Copynumber: 2.2 Consensus size: 101
61482683 CAATGATGTT
*
61482693 CGGTTCACATAGTAGCCTACACATAGTACTACACATGTGACCATTACCATTCGATACACGTAGTA
1 CGGTTCACATAGTAGCCTACACATAGTACTACACATGCGACCA-TACCATTCGATACACGTAGTA
** ** *
61482758 GCCTGTACATAGTACTACTTACGTGATCGAAACTATC
65 GCCTACACATAGTACTACACACGTGATCCAAACTATC
* * * *
61482795 CGGTACGCATAGTAGCCTGCACATAGTACTACACATGCGACC-TATCATTCTTG-TACACGTAGT
1 CGGTTCACATAGTAGCCTACACATAGTACTACACATGCGACCATACCATTC--GATACACGTAGT
* *
61482858 AGCCTACACATAGTACTACACACGTGA-CCATCACTTTC
64 AGCCTACACATAGTACTACACACGTGATCCA-AACTATC
* *
61482896 AC-TTTCACATAGTGGCCTACACA
1 -CGGTTCACATAGTAGCCTACACA
61482919 CAATCCGTGC
Statistics
Matches: 103, Mismatches: 17, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
100 9 0.09
101 54 0.52
102 40 0.39
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (101 bp):
CGGTTCACATAGTAGCCTACACATAGTACTACACATGCGACCATACCATTCGATACACGTAGTAG
CCTACACATAGTACTACACACGTGATCCAAACTATC
Found at i:61488405 original size:45 final size:45
Alignment explanation
Indices: 61488349--61488434 Score: 136
Period size: 45 Copynumber: 1.9 Consensus size: 45
61488339 CTCGGTGGAT
* *
61488349 TCAGCACATAGCAATCACCTTATTAATCAATGATGTCCGGTGAAA
1 TCAGCACATAGCAACCACCTTACTAATCAATGATGTCCGGTGAAA
* *
61488394 TCAGCACATAGCAACCACTTTACTAATCAATGATGTTCGGT
1 TCAGCACATAGCAACCACCTTACTAATCAATGATGTCCGGT
61488435 TCACATAGTA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.28
Consensus pattern (45 bp):
TCAGCACATAGCAACCACCTTACTAATCAATGATGTCCGGTGAAA
Found at i:61488574 original size:45 final size:45
Alignment explanation
Indices: 61488518--61488603 Score: 136
Period size: 45 Copynumber: 1.9 Consensus size: 45
61488508 CTCGGTGGAT
* * *
61488518 TCAGCACATAGCAATCACCTTATTAATCAATGATGTCCGGTGAAA
1 TCAGCACATAGCAACCACCTTACTAATCAATGATATCCGGTGAAA
*
61488563 TCAGCACATAGCAACCACTTTACTAATCAATGATATCCGGT
1 TCAGCACATAGCAACCACCTTACTAATCAATGATATCCGGT
61488604 ACGCATAGTA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.35, C:0.24, G:0.14, T:0.27
Consensus pattern (45 bp):
TCAGCACATAGCAACCACCTTACTAATCAATGATATCCGGTGAAA
Found at i:61488613 original size:169 final size:168
Alignment explanation
Indices: 61488333--61488669 Score: 579
Period size: 169 Copynumber: 2.0 Consensus size: 168
61488323 GGAATAATAA
61488333 CAGATACTCGGTGGATTCAGCACATAGCAATCACCTTATTAATCAATGATGTCCGGTGAAATCAG
1 CAGATACTCGGTGGATTCAGCACATAGCAATCACCTTATTAATCAATGATGTCCGGTGAAATCAG
* * *
61488398 CACATAGCAACCACTTTACTAATCAATGATGTTCGGTTCACATAGTAGCCTGCACATAGTACTAC
66 CACATAGCAACCACTTTACTAATCAATGATATCCGGTACACATAGTAGCCTGCACATAGTACTAC
*
61488463 ACATGTGACCATTACCATT-C-GATACACGTAGTAGCCTGC
131 ACATGCGACC--TACCATTCCTG-TACACGTAGTAGCCTGC
61488502 CAGATACTCGGTGGATTCAGCACATAGCAATCACCTTATTAATCAATGATGTCCGGTGAAATCAG
1 CAGATACTCGGTGGATTCAGCACATAGCAATCACCTTATTAATCAATGATGTCCGGTGAAATCAG
*
61488567 CACATAGCAACCACTTTACTAATCAATGATATCCGGTACGCATAGTAGCCTGCACATAGTACTAC
66 CACATAGCAACCACTTTACTAATCAATGATATCCGGTACACATAGTAGCCTGCACATAGTACTAC
*
61488632 ACATGCGACCTATCATTCCTGTACACGTAGTAGCCTGC
131 ACATGCGACCTACCATTCCTGTACACGTAGTAGCCTGC
61488670 ACATAGTAAT
Statistics
Matches: 160, Mismatches: 6, Indels: 5
0.94 0.04 0.03
Matches are distributed among these distances:
167 6 0.04
168 18 0.11
169 136 0.85
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (168 bp):
CAGATACTCGGTGGATTCAGCACATAGCAATCACCTTATTAATCAATGATGTCCGGTGAAATCAG
CACATAGCAACCACTTTACTAATCAATGATATCCGGTACACATAGTAGCCTGCACATAGTACTAC
ACATGCGACCTACCATTCCTGTACACGTAGTAGCCTGC
Found at i:61492292 original size:14 final size:15
Alignment explanation
Indices: 61492275--61492307 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
61492265 GTAAAATTTA
61492275 ACATAT-AGATTATG
1 ACATATAAGATTATG
*
61492289 ACATATAAGCTTATG
1 ACATATAAGATTATG
61492304 ACAT
1 ACAT
61492308 CATGTAACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.33
Consensus pattern (15 bp):
ACATATAAGATTATG
Found at i:61496246 original size:44 final size:44
Alignment explanation
Indices: 61496196--61496317 Score: 149
Period size: 44 Copynumber: 2.8 Consensus size: 44
61496186 ATCTGCTATT
*
61496196 TTCAACCTACTCCACTGTTG-CTCAAGGAGATAGGA-TTCACAATC
1 TTCAACCTACTCCACTGCTGAC-CAAGGAGATAGGACTT-ACAATC
* *
61496240 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGACTTACAATC
1 TTCAACCTACTCCACTGCTGACCAAGGAGATAGGACTTACAATC
* * * *
61496284 TTCAACCTATTCTACTGCTGTCCAGGGAGATAGG
1 TTCAACCTACTCCACTGCTGACCAAGGAGATAGG
61496318 GTTGGGGTCA
Statistics
Matches: 71, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
44 68 0.96
45 3 0.04
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.27
Consensus pattern (44 bp):
TTCAACCTACTCCACTGCTGACCAAGGAGATAGGACTTACAATC
Found at i:61496454 original size:88 final size:88
Alignment explanation
Indices: 61496328--61496546 Score: 348
Period size: 88 Copynumber: 2.5 Consensus size: 88
61496318 GTTGGGGTCA
* * *** *
61496328 TCGATCTGCTTCGCTGTCGGTGTAGGAAGGCAAAATCTGCTATTTTTAACTTGCTCCGTTACAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCAACTCCGCTACAAC
61496393 CCAGGGAGGCAAAGCTAGTGTCT
66 CCAGGGAGGCAAAGCTAGTGTCT
61496416 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCAACTCCGCTACAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCAACTCCGCTACAAC
* * *
61496481 CCAGTGAGGCAAGGCTGGTGTCT
66 CCAGGGAGGCAAAGCTAGTGTCT
*
61496504 TCAATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTAT
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTAT
61496547 CTTCACTAAT
Statistics
Matches: 121, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
88 121 1.00
ACGTcount: A:0.22, C:0.24, G:0.26, T:0.28
Consensus pattern (88 bp):
TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCAACTCCGCTACAAC
CCAGGGAGGCAAAGCTAGTGTCT
Found at i:61497896 original size:14 final size:15
Alignment explanation
Indices: 61497873--61497905 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
61497863 ATTGACGCTT
61497873 TTCCAAATAAGG-CC
1 TTCCAAATAAGGTCC
*
61497887 TTCCACATAAGGTCC
1 TTCCAAATAAGGTCC
61497902 TTCC
1 TTCC
61497906 CAGCTTGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.27, C:0.33, G:0.12, T:0.27
Consensus pattern (15 bp):
TTCCAAATAAGGTCC
Found at i:61500474 original size:22 final size:22
Alignment explanation
Indices: 61500448--61500513 Score: 54
Period size: 22 Copynumber: 3.1 Consensus size: 22
61500438 ATTGTTCGAG
61500448 CTTTTCTAATCTTTGGTCCATA
1 CTTTTCTAATCTTTGGTCCATA
*
61500470 CTTTT-TGGAA---TT-GTTCA-A
1 CTTTTCT--AATCTTTGGTCCATA
61500488 GCTTTTCTAATCTTTGGTCCATA
1 -CTTTTCTAATCTTTGGTCCATA
61500511 CTT
1 CTT
61500514 CTTAATTTCG
Statistics
Matches: 33, Mismatches: 2, Indels: 18
0.62 0.04 0.34
Matches are distributed among these distances:
18 3 0.09
19 9 0.27
20 3 0.09
21 3 0.09
22 12 0.36
23 3 0.09
ACGTcount: A:0.18, C:0.20, G:0.12, T:0.50
Consensus pattern (22 bp):
CTTTTCTAATCTTTGGTCCATA
Found at i:61500491 original size:41 final size:41
Alignment explanation
Indices: 61500429--61500513 Score: 161
Period size: 41 Copynumber: 2.1 Consensus size: 41
61500419 TCCTGTGTTT
*
61500429 CTTTTTGGAATTGTTCGAGCTTTTCTAATCTTTGGTCCATA
1 CTTTTTGGAATTGTTCAAGCTTTTCTAATCTTTGGTCCATA
61500470 CTTTTTGGAATTGTTCAAGCTTTTCTAATCTTTGGTCCATA
1 CTTTTTGGAATTGTTCAAGCTTTTCTAATCTTTGGTCCATA
61500511 CTT
1 CTT
61500514 CTTAATTTCG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.18, C:0.18, G:0.15, T:0.49
Consensus pattern (41 bp):
CTTTTTGGAATTGTTCAAGCTTTTCTAATCTTTGGTCCATA
Found at i:61502979 original size:3 final size:3
Alignment explanation
Indices: 61502966--61503006 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
61502956 GCGCATGAAT
*
61502966 ATA AAA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
61503007 GATACAAGAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:61503510 original size:19 final size:19
Alignment explanation
Indices: 61503486--61503539 Score: 90
Period size: 19 Copynumber: 2.8 Consensus size: 19
61503476 AATCATATCT
*
61503486 TCTAAGATTGCATATTATA
1 TCTAAGATTGCATATCATA
*
61503505 TCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATA
61503524 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
61503540 CTTAAAGATT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.37, C:0.15, G:0.09, T:0.39
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:61504617 original size:23 final size:24
Alignment explanation
Indices: 61504547--61504625 Score: 70
Period size: 23 Copynumber: 3.2 Consensus size: 24
61504537 CTACTATAAT
* *
61504547 ATAAACATAAAAAATTATTAAGATA
1 ATAAATATATAAAATTATTAA-ATA
* ** *
61504572 ATTATATATATAATTTTAGTAAATA
1 A-TAAATATATAAAATTATTAAATA
61504597 A-AAATATATAAAATTATTAAATA
1 ATAAATATATAAAATTATTAAATA
*
61504620 TTAAAT
1 ATAAAT
61504626 TAAAATAATA
Statistics
Matches: 41, Mismatches: 11, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
23 18 0.44
24 4 0.10
25 5 0.12
26 14 0.34
ACGTcount: A:0.58, C:0.01, G:0.03, T:0.38
Consensus pattern (24 bp):
ATAAATATATAAAATTATTAAATA
Found at i:61507899 original size:161 final size:161
Alignment explanation
Indices: 61507716--61508037 Score: 635
Period size: 161 Copynumber: 2.0 Consensus size: 161
61507706 TAAAACAAAA
61507716 GAAGAAAATAAGCTTCATCTCTTTCATTCTTTTCATTTTCCAAAGTCGAACCACCATTAGAGGAC
1 GAAGAAAATAAGCTTCATCTCTTTCATTCTTTTCATTTTCCAAAGTCGAACCACCATTAGAGGAC
61507781 CTTGAAGCTTCGGCTTTAATTTTCTTCTTGCATGTAAGTGATTTTCCTACCCGTTTCTTGTAATT
66 CTTGAAGCTTCGGCTTTAATTTTCTTCTTGCATGTAAGTGATTTTCCTACCCGTTTCTTGTAATT
61507846 TTTATGTTTTTGATATTATTGCAACTAGGTT
131 TTTATGTTTTTGATATTATTGCAACTAGGTT
61507877 GAAGAAAATAAGCTTCATCTCTTTCATTCTTTTCATTTTCCAAAGTCGAACCACCATTAGAGGAC
1 GAAGAAAATAAGCTTCATCTCTTTCATTCTTTTCATTTTCCAAAGTCGAACCACCATTAGAGGAC
*
61507942 CTTGAAGCTTCGGCTTTAATTTTCTTCTTGCATGTAAGTGATTTTCCTACTCGTTTCTTGTAATT
66 CTTGAAGCTTCGGCTTTAATTTTCTTCTTGCATGTAAGTGATTTTCCTACCCGTTTCTTGTAATT
61508007 TTTATGTTTTTGATATTATTGCAACTAGGTT
131 TTTATGTTTTTGATATTATTGCAACTAGGTT
61508038 CAGCTAACTT
Statistics
Matches: 160, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
161 160 1.00
ACGTcount: A:0.24, C:0.18, G:0.14, T:0.43
Consensus pattern (161 bp):
GAAGAAAATAAGCTTCATCTCTTTCATTCTTTTCATTTTCCAAAGTCGAACCACCATTAGAGGAC
CTTGAAGCTTCGGCTTTAATTTTCTTCTTGCATGTAAGTGATTTTCCTACCCGTTTCTTGTAATT
TTTATGTTTTTGATATTATTGCAACTAGGTT
Found at i:61515178 original size:16 final size:19
Alignment explanation
Indices: 61515147--61515184 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
61515137 GGAATTAGAA
61515147 TTAAGTTGAGAAAATT-AT
1 TTAAGTTGAGAAAATTCAT
61515165 TTAA-TTGA-AAAATTCAT
1 TTAAGTTGAGAAAATTCAT
61515182 TTA
1 TTA
61515185 TCTAATTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 6 0.32
17 9 0.47
18 4 0.21
ACGTcount: A:0.45, C:0.03, G:0.11, T:0.42
Consensus pattern (19 bp):
TTAAGTTGAGAAAATTCAT
Found at i:61519003 original size:20 final size:20
Alignment explanation
Indices: 61518978--61519017 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
61518968 CATTTCATTT
**
61518978 ATGCAATTGTTTTATCCATA
1 ATGCAATTACTTTATCCATA
61518998 ATGCAATTACTTTATCCATA
1 ATGCAATTACTTTATCCATA
61519018 CCATATTCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.17, G:0.07, T:0.42
Consensus pattern (20 bp):
ATGCAATTACTTTATCCATA
Found at i:61519246 original size:37 final size:40
Alignment explanation
Indices: 61519191--61519299 Score: 125
Period size: 41 Copynumber: 2.8 Consensus size: 40
61519181 TAATTCGAAG
* *
61519191 TAATAAATTGACATCCAGTGTCTCATCG-GTTAAACC-AA
1 TAATAAATTGACACCCAGTGTCTCATCGAATTAAACCAAA
* * * *
61519229 -AGTAAATTGGCACCCAGTGCCTCATCGAATTAATCCGAAA
1 TAATAAATTGACACCCAGTGTCTCATCGAATTAAACC-AAA
*
61519269 TAATAAATTGACACCTAGTGTCTCATCGAAT
1 TAATAAATTGACACCCAGTGTCTCATCGAAT
61519300 CGAAGTCGAA
Statistics
Matches: 57, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
37 23 0.40
38 6 0.11
40 2 0.04
41 26 0.46
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.28
Consensus pattern (40 bp):
TAATAAATTGACACCCAGTGTCTCATCGAATTAAACCAAA
Found at i:61519294 original size:41 final size:40
Alignment explanation
Indices: 61519172--61519299 Score: 122
Period size: 41 Copynumber: 3.2 Consensus size: 40
61519162 CACCCAATGC
* * *
61519172 CTCATTGAA-TAATTCGAAGTAATAAATTGACATCCAGTGT
1 CTCATCGAATTAATCCGAAATAATAAATTGACA-CCAGTGT
* * * * *
61519212 CTCATCG-GTTAAACC--AA-AGTAAATTGGCACCCAGTGC
1 CTCATCGAATTAATCCGAAATAATAAATTGACA-CCAGTGT
61519249 CTCATCGAATTAATCCGAAATAATAAATTGACACCTAGTGT
1 CTCATCGAATTAATCCGAAATAATAAATTGACACC-AGTGT
61519290 CTCATCGAAT
1 CTCATCGAAT
61519300 CGAAGTCGAA
Statistics
Matches: 68, Mismatches: 14, Indels: 11
0.73 0.15 0.12
Matches are distributed among these distances:
37 23 0.34
38 7 0.10
40 14 0.21
41 24 0.35
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (40 bp):
CTCATCGAATTAATCCGAAATAATAAATTGACACCAGTGT
Found at i:61519497 original size:24 final size:24
Alignment explanation
Indices: 61519452--61519498 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
61519442 TATATATACC
61519452 AATTCAATCAATATAAATTCAATA
1 AATTCAATCAATATAAATTCAATA
61519476 AATTC-ATCACATACTAAA-TCAAT
1 AATTCAATCA-ATA-TAAATTCAAT
61519499 TCATTTCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.19
24 13 0.62
25 4 0.19
ACGTcount: A:0.51, C:0.17, G:0.00, T:0.32
Consensus pattern (24 bp):
AATTCAATCAATATAAATTCAATA
Found at i:61520024 original size:4 final size:4
Alignment explanation
Indices: 61520015--61520106 Score: 64
Period size: 4 Copynumber: 22.5 Consensus size: 4
61520005 ACTTTTCTCC
*
61520015 TTCT TTCT TTCT TTTT TTCTT TTCT TTCT TTCAT TTCT TTCCT TCTCT
1 TTCT TTCT TTCT TTCT TTC-T TTCT TTCT TTC-T TTCT TT-CT T-TCT
* * * * *
61520063 GT-T TTGT TTCT TTCT CTCA TTCT TT-T TCTAT TTCT TT-T TTCT TT
1 TTCT TTCT TTCT TTCT TTCT TTCT TTCT T-TCT TTCT TTCT TTCT TT
61520107 TACTTTATCA
Statistics
Matches: 70, Mismatches: 10, Indels: 16
0.73 0.10 0.17
Matches are distributed among these distances:
3 7 0.10
4 47 0.67
5 15 0.21
6 1 0.01
ACGTcount: A:0.03, C:0.22, G:0.02, T:0.73
Consensus pattern (4 bp):
TTCT
Found at i:61520183 original size:35 final size:36
Alignment explanation
Indices: 61520120--61520211 Score: 89
Period size: 35 Copynumber: 2.5 Consensus size: 36
61520110 TTTATCATTA
* * * *
61520120 TAATATAATAATATGTATACTTAAA-TTTTAAGTTT
1 TAATATTATAATATATATAATTAAATTTTTAACTTT
*
61520155 TAATATTATAATAT-TATAATATATATTTTTTAACTTT
1 TAATATTATAATATATATAAT-TA-AATTTTTAACTTT
*
61520192 AAATATTTATAATATATATA
1 TAATA-TTATAATATATATA
61520212 CACTTATGCC
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
34 5 0.11
35 15 0.32
36 1 0.02
37 13 0.28
38 9 0.19
39 4 0.09
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (36 bp):
TAATATTATAATATATATAATTAAATTTTTAACTTT
Found at i:61524980 original size:41 final size:40
Alignment explanation
Indices: 61524856--61524991 Score: 143
Period size: 37 Copynumber: 3.5 Consensus size: 40
61524846 ACCAGTTTGG
** *
61524856 CACCCAGTGCCTCATCGAATAATTTGAAGTAATAAATTAA
1 CACCCAGTGCCTCATCGAATAATCCGAAGTAATAAATTGA
* ** * *
61524896 CACCCAGTGTCTCATCGGTTAAACC-AA--AATAAATTGG
1 CACCCAGTGCCTCATCGAATAATCCGAAGTAATAAATTGA
61524933 CACCCAGTGCCTCATCGAACTAATCCGAAGTAATAAATTGA
1 CACCCAGTGCCTCATCGAA-TAATCCGAAGTAATAAATTGA
** *
61524974 TTCCCAGTGTCTCATCGA
1 CACCCAGTGCCTCATCGA
61524992 CTCGAAGTCG
Statistics
Matches: 76, Mismatches: 16, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
37 24 0.32
38 5 0.07
39 4 0.05
40 19 0.25
41 24 0.32
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.26
Consensus pattern (40 bp):
CACCCAGTGCCTCATCGAATAATCCGAAGTAATAAATTGA
Found at i:61525194 original size:24 final size:24
Alignment explanation
Indices: 61525149--61525195 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
61525139 TATATATACC
61525149 AATTCAATCAATATAAATTCAATA
1 AATTCAATCAATATAAATTCAATA
61525173 AATTC-ATCACATACTAAA-TCAAT
1 AATTCAATCA-ATA-TAAATTCAAT
61525196 CCATTTCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.19
24 13 0.62
25 4 0.19
ACGTcount: A:0.51, C:0.17, G:0.00, T:0.32
Consensus pattern (24 bp):
AATTCAATCAATATAAATTCAATA
Found at i:61526705 original size:16 final size:15
Alignment explanation
Indices: 61526684--61526713 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
61526674 ATTGTGTAAA
61526684 ATTAATTAATATAATT
1 ATTAATTAAT-TAATT
61526700 ATTAATTAATTAAT
1 ATTAATTAATTAAT
61526714 ATTTTGAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTAATTAATTAATT
Found at i:61530054 original size:20 final size:22
Alignment explanation
Indices: 61530014--61530054 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
61530004 ATATTAAAAA
*
61530014 ATATTTTTAATTGATATTTTAT
1 ATATTTTTAATTGATAATTTAT
61530036 ATATTTTTAATT-A-AATTTA
1 ATATTTTTAATTGATAATTTA
61530055 AATAATATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 1 0.06
22 12 0.67
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (22 bp):
ATATTTTTAATTGATAATTTAT
Found at i:61531548 original size:18 final size:19
Alignment explanation
Indices: 61531520--61531555 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
61531510 GTTTTTACCA
*
61531520 TTTTTAGTAATATTTTTAC
1 TTTTTAGTAATATATTTAC
61531539 TTTTTA-TAATATATTTA
1 TTTTTAGTAATATATTTA
61531556 ATTAAAATCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (19 bp):
TTTTTAGTAATATATTTAC
Found at i:61531839 original size:28 final size:28
Alignment explanation
Indices: 61531808--61531862 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 28
61531798 TTTTCAATTT
* *
61531808 TTTATAATTATATATTTGAAATTTAATA
1 TTTACAATTATATATTTAAAATTTAATA
* * *
61531836 TTTACACTTTTATTTTTAAAATTTAAT
1 TTTACAATTATATATTTAAAATTTAAT
61531863 GTTTCTATTT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (28 bp):
TTTACAATTATATATTTAAAATTTAATA
Done.